3s2h - Revision history

OCA at 12:44, 14 March 2024

OCA — Thu, 14 Mar 2024 12:44:06 GMT

←Older revision		Revision as of 12:44, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3s2h' size='340' side='right'caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3s2h' size='340' side='right'caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s2h]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae~~ Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S2H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s2h]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S2H FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=2IA:2-DEOXY-2-IODOADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>2IA</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2IA:2-DEOXY-2-IODOADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>2IA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3s1m\|3s1m]]~~, ~~[[3rzo\|3rzo]], [[3s1n\|3s1n]], [[3s1q\|3s1q]], [[3s1r\|3s1r]], [[3s2d\|3s2d]], [[3rzd\|3rzd]], [[3s14\|3s14]], [[3s15\|3s15]], [[3s16\|3s16]], [[3s17\|3s17]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [https://pdbe.org/3s2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [https://www.ebi.ac.uk/pdbsum/3s2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s2h ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [https://pdbe.org/3s2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [https://www.ebi.ac.uk/pdbsum/3s2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s2h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[https://www.uniprot.org/uniprot/RPB3_YEAST RPB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination. [[https://www.uniprot.org/uniprot/RPB9_YEAST RPB9_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template. Involved in the regulation of transcription elongation. Involved in DNA repair of damage in the transcribed strand. Mediates a transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER).<ref>PMID:12411509</ref> [[https://www.uniprot.org/uniprot/RPB11_YEAST RPB11_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft. Seems to be involved transcript termination. [[https://www.uniprot.org/uniprot/RPB2_YEAST RPB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it. [[https://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[https://www.uniprot.org/uniprot/RPB1_YEAST RPB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA. [[https://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity). [[https://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[https://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity).	+	[https://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the RNA is detectable; a second state with 4- and 5-nucleotide RNAs, with an RNA-DNA hybrid in a grossly distorted conformation; and a third state with RNAs of 6 nucleotides and longer, essentially the same as a stable elongating complex. The transition from the first to the second state correlates with a markedly reduced frequency of abortive initiation. The transition from the second to the third state correlates with partial "bubble collapse" and promoter escape. Polymerase structure is permissive for abortive initiation, thereby setting a lower limit on polymerase-promoter complex lifetime and allowing the dissociation of nonspecific complexes. Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control.	+
-		+
-	~~Initiation complex structure and promoter proofreading.,Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD Science. 2011 Jul 29;333(6042):633-7. PMID:21798951<ref>PMID:21798951</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3s2h" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Saccharomyces cerevisiae]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Bushnell~~, D A~~]]	+	[[Category: Bushnell DA]]
-	[[Category: Huang, X]]	+	[[Category: Huang X]]
-	[[Category: Kornberg~~, R D~~]]	+	[[Category: Kornberg RD]]
-	[[Category: Liu, X]]	+	[[Category: Liu X]]
-	[[Category: Silva~~, D A]]~~	+	[[Category: Silva DA]]
-	~~[[Category: Initiation complex]]~~	+
-	~~[[Category: Rna polymerase ii]]~~	+
-	~~[[Category: Transcription-rna-dna complex~~]]	+

OCA at 10:35, 22 June 2022

OCA — Wed, 22 Jun 2022 10:35:12 GMT

←Older revision		Revision as of 10:35, 22 June 2022
Line 3:		Line 3:
	<StructureSection load='3s2h' size='340' side='right'caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3s2h' size='340' side='right'caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s2h]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S2H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s2h]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S2H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2IA:2-DEOXY-2-IODOADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>2IA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2IA:2-DEOXY-2-IODOADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>2IA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s1m\|3s1m]], [[3rzo\|3rzo]], [[3s1n\|3s1n]], [[3s1q\|3s1q]], [[3s1r\|3s1r]], [[3s2d\|3s2d]], [[3rzd\|3rzd]], [[3s14\|3s14]], [[3s15\|3s15]], [[3s16\|3s16]], [[3s17\|3s17]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3s1m\|3s1m]], [[3rzo\|3rzo]], [[3s1n\|3s1n]], [[3s1q\|3s1q]], [[3s1r\|3s1r]], [[3s2d\|3s2d]], [[3rzd\|3rzd]], [[3s14\|3s14]], [[3s15\|3s15]], [[3s16\|3s16]], [[3s17\|3s17]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [~~http~~://pdbe.org/3s2h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s2h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s2h ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [https://pdbe.org/3s2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [https://www.ebi.ac.uk/pdbsum/3s2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s2h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[~~http~~://www.uniprot.org/uniprot/RPB3_YEAST RPB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination. [[~~http~~://www.uniprot.org/uniprot/RPB9_YEAST RPB9_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template. Involved in the regulation of transcription elongation. Involved in DNA repair of damage in the transcribed strand. Mediates a transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER).<ref>PMID:12411509</ref> [[~~http~~://www.uniprot.org/uniprot/RPB11_YEAST RPB11_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft. Seems to be involved transcript termination. [[~~http~~://www.uniprot.org/uniprot/RPB2_YEAST RPB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it. [[~~http~~://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[~~http~~://www.uniprot.org/uniprot/RPB1_YEAST RPB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA. [[~~http~~://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity). [[~~http~~://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[~~http~~://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity).	+	[[https://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[https://www.uniprot.org/uniprot/RPB3_YEAST RPB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination. [[https://www.uniprot.org/uniprot/RPB9_YEAST RPB9_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template. Involved in the regulation of transcription elongation. Involved in DNA repair of damage in the transcribed strand. Mediates a transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER).<ref>PMID:12411509</ref> [[https://www.uniprot.org/uniprot/RPB11_YEAST RPB11_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft. Seems to be involved transcript termination. [[https://www.uniprot.org/uniprot/RPB2_YEAST RPB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it. [[https://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[https://www.uniprot.org/uniprot/RPB1_YEAST RPB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA. [[https://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity). [[https://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[https://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:55, 14 August 2019

OCA — Wed, 14 Aug 2019 17:55:10 GMT

←Older revision		Revision as of 17:55, 14 August 2019
Line 1:		Line 1:

	==RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP==		==RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP==
-	<StructureSection load='3s2h' size='340' side='right' caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='3s2h' size='340' side='right'caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3s2h]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S2H FirstGlance]. <br>		<table><tr><td colspan='2'>[[3s2h]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S2H FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3s2h" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3s2h" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Bushnell, D A]]		[[Category: Bushnell, D A]]

OCA at 09:32, 8 November 2017

OCA — Wed, 08 Nov 2017 09:32:26 GMT

←Older revision		Revision as of 09:32, 8 November 2017
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3s2h" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3s2h" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:26, 5 August 2016

OCA — Fri, 05 Aug 2016 13:26:20 GMT

←Older revision		Revision as of 13:26, 5 August 2016
Line 1:		Line 1:
		+
	==RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP==		==RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP==
	<StructureSection load='3s2h' size='340' side='right' caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3s2h' size='340' side='right' caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s1m\|3s1m]], [[3rzo\|3rzo]], [[3s1n\|3s1n]], [[3s1q\|3s1q]], [[3s1r\|3s1r]], [[3s2d\|3s2d]], [[3rzd\|3rzd]], [[3s14\|3s14]], [[3s15\|3s15]], [[3s16\|3s16]], [[3s17\|3s17]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s1m\|3s1m]], [[3rzo\|3rzo]], [[3s1n\|3s1n]], [[3s1q\|3s1q]], [[3s1r\|3s1r]], [[3s2d\|3s2d]], [[3rzd\|3rzd]], [[3s14\|3s14]], [[3s15\|3s15]], [[3s16\|3s16]], [[3s17\|3s17]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [http://www.ebi.ac.uk/pdbsum/3s2h PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [http://pdbe.org/3s2h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [http://www.ebi.ac.uk/pdbsum/3s2h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s2h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3s2h" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 02:50, 25 December 2014

OCA — Thu, 25 Dec 2014 02:50:56 GMT

←Older revision		Revision as of 02:50, 25 December 2014
Line 9:		Line 9:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [http://www.ebi.ac.uk/pdbsum/3s2h PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [http://www.ebi.ac.uk/pdbsum/3s2h PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPB3_YEAST RPB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination. [[http://www.uniprot.org/uniprot/RPB9_YEAST RPB9_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template. Involved in the regulation of transcription elongation. Involved in DNA repair of damage in the transcribed strand. Mediates a transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER).<ref>PMID:12411509</ref> [[http://www.uniprot.org/uniprot/RPB11_YEAST RPB11_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft. Seems to be involved transcript termination. [[http://www.uniprot.org/uniprot/RPB2_YEAST RPB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it. [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPB1_YEAST RPB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA. [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity). [[http://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[http://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 11:18, 9 December 2014

OCA — Tue, 09 Dec 2014 11:18:48 GMT

←Older revision		Revision as of 11:18, 9 December 2014
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-	[[~~Image:~~3s2h.~~png~~\|~~left~~\|~~200px~~]]	+	==RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP==
		+	<StructureSection load='3s2h' size='340' side='right' caption='[[3s2h]], [[Resolution\|resolution]] 3.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3s2h]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S2H FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2IA:2-DEOXY-2-IODOADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>2IA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s1m\|3s1m]], [[3rzo\|3rzo]], [[3s1n\|3s1n]], [[3s1q\|3s1q]], [[3s1r\|3s1r]], [[3s2d\|3s2d]], [[3rzd\|3rzd]], [[3s14\|3s14]], [[3s15\|3s15]], [[3s16\|3s16]], [[3s17\|3s17]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s2h RCSB], [http://www.ebi.ac.uk/pdbsum/3s2h PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the RNA is detectable; a second state with 4- and 5-nucleotide RNAs, with an RNA-DNA hybrid in a grossly distorted conformation; and a third state with RNAs of 6 nucleotides and longer, essentially the same as a stable elongating complex. The transition from the first to the second state correlates with a markedly reduced frequency of abortive initiation. The transition from the second to the third state correlates with partial "bubble collapse" and promoter escape. Polymerase structure is permissive for abortive initiation, thereby setting a lower limit on polymerase-promoter complex lifetime and allowing the dissociation of nonspecific complexes. Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control.

-	~~{{STRUCTURE_3s2h\| PDB=3s2h \| SCENE= }}~~	+	Initiation complex structure and promoter proofreading.,Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD Science. 2011 Jul 29;333(6042):633-7. PMID:21798951<ref>PMID:21798951</ref>

-	~~===RNA Polymerase II Initiation Complex with~~ a ~~6-nt RNA containing a 2[prime]-iodo ATP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21798951}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3s2h]] is a 12 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021798951<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Bushnell, D A.]]	+	[[Category: Bushnell, D A]]
-	[[Category: Huang, X.]]	+	[[Category: Huang, X]]
-	[[Category: Kornberg, R D.]]	+	[[Category: Kornberg, R D]]
-	[[Category: Liu, X.]]	+	[[Category: Liu, X]]
-	[[Category: Silva, D A.]]	+	[[Category: Silva, D A]]
	[[Category: Initiation complex]]		[[Category: Initiation complex]]
	[[Category: Rna polymerase ii]]		[[Category: Rna polymerase ii]]
	[[Category: Transcription-rna-dna complex]]		[[Category: Transcription-rna-dna complex]]

OCA at 11:49, 20 October 2012

OCA — Sat, 20 Oct 2012 11:49:13 GMT

←Older revision		Revision as of 11:49, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3s2h]] is a 12 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA].	+	[[3s2h]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA].

	==See Also==		==See Also==

OCA at 06:42, 26 July 2012

OCA — Thu, 26 Jul 2012 06:42:13 GMT

←Older revision		Revision as of 06:42, 26 July 2012
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-	[[Image:3s2h.~~jpg~~\|left\|200px]]	+	[[Image:3s2h.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3s2h", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_3s2h\| PDB=3s2h \| SCENE= }}		{{STRUCTURE_3s2h\| PDB=3s2h \| SCENE= }}

	===RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP===		===RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21798951}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21798951 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21798951}}		{{ABSTRACT_PUBMED_21798951}}

	==About this Structure==		==About this Structure==
-	[[3s2h]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA].	+	[[3s2h]] is a 12 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==

OCA at 06:12, 17 August 2011

OCA — Wed, 17 Aug 2011 06:12:47 GMT

←Older revision		Revision as of 06:12, 17 August 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3s2h.jpg\|left\|200px]]

-	The ~~entry 3s2h~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s2h", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3s2h\| PDB=3s2h \| SCENE= }}

-	~~Authors: Liu, X., Bushnell, D.A., Silva, D.A., Huang, X., Kornberg, R.D.~~	+	===RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP===

-	~~Description~~: ~~RNA Polymerase II Initiation Complex with~~ a 6-nt RNA ~~containing a 2~~[~~prime~~]-~~iodo ATP~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21798951}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21798951 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21798951}}
		+
		+	==About this Structure==
		+	[[3s2h]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2H OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021798951</ref><references group="xtra"/>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Bushnell, D A.]]
		+	[[Category: Huang, X.]]
		+	[[Category: Kornberg, R D.]]
		+	[[Category: Liu, X.]]
		+	[[Category: Silva, D A.]]
		+	[[Category: Initiation complex]]
		+	[[Category: Rna polymerase ii]]
		+	[[Category: Transcription-rna-dna complex]]