5xog - Revision history

OCA at 10:19, 27 March 2024

OCA — Wed, 27 Mar 2024 10:19:26 GMT

←Older revision		Revision as of 10:19, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5xog' size='340' side='right'caption='[[5xog]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5xog' size='340' side='right'caption='[[5xog]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xog]] is a 17 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/ ~~], [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_atcc_76273_/_cbs_7435_/_cect_11047_/_nrrl_y-11430_/_wegner_21-1)~~ Komagataella phaffii ~~(strain atcc 76273 / cbs~~ 7435 ~~/ cect 11047 / nrrl y-11430 / wegner 21-1)~~] and [~~http~~://en.wikipedia.org/wiki/~~Komagataella_phaffii_(strain_gs115_/_atcc_20864)~~ Komagataella phaffii ~~(strain gs115 / atcc 20864)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XOG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XOG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xog]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Komagataella_phaffii_CBS_7435 Komagataella phaffii CBS 7435] and [https://en.wikipedia.org/wiki/Komagataella_phaffii_GS115 Komagataella phaffii GS115]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XOG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <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]] 3Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5xog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xog OCA], [~~http~~://pdbe.org/5xog PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xog RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xog PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xog 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=5xog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xog OCA], [https://pdbe.org/5xog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xog RCSB], [https://www.ebi.ac.uk/pdbsum/5xog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xog ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/F2QPE6_KOMPC F2QPE6_KOMPC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586] [[http://www.uniprot.org/uniprot/C4QZQ7_KOMPG C4QZQ7_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] [[http://www.uniprot.org/uniprot/A0A1B2JER8_PICPA A0A1B2JER8_PICPA]] Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.[RuleBase:RU364033]	+	[https://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex (EC) for processive transcription. Here, we report the structure of the Pol II EC bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing the "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel". The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel", directing the exiting nascent RNA. Thus, the EC establishes a completely different transcription/regulation platform from that of the initiation complexes.	+
-		+
-	Structure of the complete elongation complex of RNA polymerase II with basal factors.,Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI Science. 2017 Aug 3. pii: eaan8552. doi: 10.1126/science.aan8552. PMID:28775211<ref>PMID:28775211</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5xog" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]		*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	*[[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: Komagataella phaffii CBS 7435]]
		+	[[Category: Komagataella phaffii GS115]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ehara, H]]	+	[[Category: Ehara H]]
-	[[Category: Sekine, S]]	+	[[Category: Sekine S]]
-	[[Category: Shirouzu, M]]	+	[[Category: Shirouzu M]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 06:55, 14 October 2020

OCA — Wed, 14 Oct 2020 06:55:54 GMT

←Older revision		Revision as of 06:55, 14 October 2020
Line 1:		Line 1:

	==RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1==		==RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1==
-	<StructureSection load='5xog' size='340' side='right' caption='[[5xog]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5xog' size='340' side='right'caption='[[5xog]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xog]] is a 17 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_atcc_76273_/_cbs_7435_/_cect_11047_/_nrrl_y-11430_/_wegner_21-1) Komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1)] and [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XOG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XOG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xog]] is a 17 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_atcc_76273_/_cbs_7435_/_cect_11047_/_nrrl_y-11430_/_wegner_21-1) Komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1)] and [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XOG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XOG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <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=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5xog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xog OCA], [http://pdbe.org/5xog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xog RCSB], [http://www.ebi.ac.uk/pdbsum/5xog PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xog ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xog OCA], [http://pdbe.org/5xog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xog RCSB], [http://www.ebi.ac.uk/pdbsum/5xog PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xog ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5xog" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xog" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Ehara, H]]		[[Category: Ehara, H]]
	[[Category: Sekine, S]]		[[Category: Sekine, S]]

OCA at 23:37, 15 November 2017

OCA — Wed, 15 Nov 2017 23:37:47 GMT

←Older revision		Revision as of 23:37, 15 November 2017
Line 9:		Line 9:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/C4QZQ7_KOMPG C4QZQ7_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] [[http://www.uniprot.org/uniprot/A0A1B2JER8_PICPA A0A1B2JER8_PICPA]] Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.[RuleBase:RU364033] [[http://www.uniprot.org/uniprot/F2QPE6_KOMPC F2QPE6_KOMPC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586]	+	[[http://www.uniprot.org/uniprot/F2QPE6_KOMPC F2QPE6_KOMPC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586] [[http://www.uniprot.org/uniprot/C4QZQ7_KOMPG C4QZQ7_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] [[http://www.uniprot.org/uniprot/A0A1B2JER8_PICPA A0A1B2JER8_PICPA]] Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.[RuleBase:RU364033]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA: Protected "5xog" [edit=sysop:move=sysop]

OCA — Thu, 24 Aug 2017 11:12:47 GMT

Protected "5xog" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:12, 24 August 2017

OCA: New page: ==RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1==
OCA — Thu, 24 Aug 2017 11:12:45 GMT

New page: ==RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1== <StructureSection load='5xog' size='340' side='right' caption='5xog, resolution 3.00Å' scen...

New page

==RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1==
<StructureSection load='5xog' size='340' side='right' caption='[[5xog]], [[Resolution|resolution]] 3.00Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5xog]] is a 17 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_atcc_76273_/_cbs_7435_/_cect_11047_/_nrrl_y-11430_/_wegner_21-1) Komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1)] and [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XOG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XOG FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5xog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xog OCA], [http://pdbe.org/5xog PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xog RCSB], [http://www.ebi.ac.uk/pdbsum/5xog PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xog ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/C4QZQ7_KOMPG C4QZQ7_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] [[http://www.uniprot.org/uniprot/A0A1B2JER8_PICPA A0A1B2JER8_PICPA]] Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.[RuleBase:RU364033] [[http://www.uniprot.org/uniprot/F2QPE6_KOMPC F2QPE6_KOMPC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex (EC) for processive transcription. Here, we report the structure of the Pol II EC bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing the "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel". The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel", directing the exiting nascent RNA. Thus, the EC establishes a completely different transcription/regulation platform from that of the initiation complexes.

Structure of the complete elongation complex of RNA polymerase II with basal factors.,Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI Science. 2017 Aug 3. pii: eaan8552. doi: 10.1126/science.aan8552. PMID:28775211<ref>PMID:28775211</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5xog" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: DNA-directed RNA polymerase]]
[[Category: Ehara, H]]
[[Category: Sekine, S]]
[[Category: Shirouzu, M]]
[[Category: Complex]]
[[Category: Transcription]]