2o5i - Revision history

OCA at 10:31, 30 August 2023

OCA — Wed, 30 Aug 2023 10:31:26 GMT

←Older revision		Revision as of 10:31, 30 August 2023
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	<StructureSection load='2o5i' size='340' side='right'caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2o5i' size='340' side='right'caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thermus_thermophilus~~ Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O5I 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]] 2.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2o5j\|2o5j]]~~</~~div~~><~~/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~~='~~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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [https://pdbe.org/2o5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [https://www.ebi.ac.uk/pdbsum/2o5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5i 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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [https://pdbe.org/2o5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [https://www.ebi.ac.uk/pdbsum/2o5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	~~[[https://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [~~[https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[https://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[https://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	+	[https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Thermus thermophilus]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Tahirov~~, T H~~]]	+	[[Category: Tahirov TH]]
-	[[Category: Vassylyev~~, D G~~]]	+	[[Category: Vassylyev DG]]
-	[[Category: Vassylyeva~~, M N]]~~	+	[[Category: Vassylyeva MN]]
-	~~[[Category: Elongation complex]]~~	+
-	~~[[Category: Non-template dna]]~~	+
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Rna transcript]]~~	+
-	~~[[Category: Template dna]]~~	+
-	~~[[Category: Transferase-dna-rna hybrid complex~~]]	+

OCA at 07:49, 2 March 2022

OCA — Wed, 02 Mar 2022 07:49:51 GMT

←Older revision		Revision as of 07:49, 2 March 2022
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	<StructureSection load='2o5i' size='340' side='right'caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2o5i' size='340' side='right'caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2O5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O5I 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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o5j\|2o5j]]</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~~://proteopedia.org/fgij/fg.htm?mol=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [~~http~~://pdbe.org/2o5i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2o5i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5i 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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [https://pdbe.org/2o5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [https://www.ebi.ac.uk/pdbsum/2o5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[~~http~~://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[~~http~~://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[~~http~~://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	+	[[https://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[https://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[https://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:57, 27 May 2020

OCA — Wed, 27 May 2020 07:57:27 GMT

←Older revision		Revision as of 07:57, 27 May 2020
Line 1:		Line 1:

	==Crystal structure of the T. thermophilus RNA polymerase elongation complex==		==Crystal structure of the T. thermophilus RNA polymerase elongation complex==
-	<StructureSection load='2o5i' size='340' side='right' caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2o5i' size='340' side='right'caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2O5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2O5I 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://pdbe.org/2o5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5i 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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://pdbe.org/2o5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Tahirov, T H]]		[[Category: Tahirov, T H]]

OCA at 06:58, 22 August 2018

OCA — Wed, 22 Aug 2018 06:58:23 GMT

←Older revision		Revision as of 06:58, 22 August 2018
Line 1:		Line 1:
		+
	==Crystal structure of the T. thermophilus RNA polymerase elongation complex==		==Crystal structure of the T. thermophilus RNA polymerase elongation complex==
	<StructureSection load='2o5i' size='340' side='right' caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2o5i' size='340' side='right' caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://pdbe.org/2o5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i 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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://pdbe.org/2o5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o5i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o5/2o5i_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o5/2o5i_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2o5i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 33:
	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-	*[[Temp1\|Temp1]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:39, 11 September 2015

OCA — Fri, 11 Sep 2015 13:39:14 GMT

←Older revision		Revision as of 13:39, 11 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i 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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://pdbe.org/2o5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2o5i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
		+	*[[Temp1\|Temp1]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:11, 25 December 2014

OCA — Thu, 25 Dec 2014 17:11:57 GMT

←Older revision		Revision as of 17:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O5I FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O5I FirstGlance]. <br>
-	</td></tr><tr><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><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i 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=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity). [[http://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Tahirov, T H.]]	+	[[Category: Tahirov, T H]]
-	[[Category: Vassylyev, D G.]]	+	[[Category: Vassylyev, D G]]
-	[[Category: Vassylyeva, M N.]]	+	[[Category: Vassylyeva, M N]]
	[[Category: Elongation complex]]		[[Category: Elongation complex]]
	[[Category: Non-template dna]]		[[Category: Non-template dna]]

OCA at 04:33, 29 September 2014

OCA — Mon, 29 Sep 2014 04:33:14 GMT

←Older revision		Revision as of 04:33, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2o5i.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the T. thermophilus RNA polymerase elongation complex==
		+	<StructureSection load='2o5i' size='340' side='right' caption='[[2o5i]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2o5i]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O5I FirstGlance]. <br>
		+	</td></tr><tr><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><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o5j\|2o5j]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o5i RCSB], [http://www.ebi.ac.uk/pdbsum/2o5i PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o5/2o5i_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the mechanisms of elongation and its regulation requires detailed information about the structural organization of the EC. Here we report the 2.5-A resolution structure of the Thermus thermophilus EC; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can specifically bind to the EC. The upstream edge of the RNA/DNA hybrid stacks on the beta'-subunit 'lid' loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination.

-	~~{{STRUCTURE_2o5i\| PDB=2o5i \| SCENE= }}~~	+	Structural basis for transcription elongation by bacterial RNA polymerase.,Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I Nature. 2007 Jul 12;448(7150):157-62. Epub 2007 Jun 20. PMID:17581590<ref>PMID:17581590</ref>

-	~~===Crystal structure~~ of the T. ~~thermophilus RNA polymerase elongation complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17581590}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2o5i]] is a 16 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017581590<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 19:18, 20 October 2012

OCA — Sat, 20 Oct 2012 19:18:47 GMT

←Older revision		Revision as of 19:18, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2o5i]] is a 16 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA].	+	[[2o5i]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA].

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

OCA: Protected "2o5i" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 06:57:11 GMT

Protected "2o5i" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:57, 27 July 2012

OCA at 06:57, 27 July 2012

OCA — Fri, 27 Jul 2012 06:57:09 GMT

←Older revision		Revision as of 06:57, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2o5i.png\|left\|200px]]		[[Image:2o5i.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2o5i", 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_2o5i\| PDB=2o5i \| SCENE= }}		{{STRUCTURE_2o5i\| PDB=2o5i \| SCENE= }}

	===Crystal structure of the T. thermophilus RNA polymerase elongation complex===		===Crystal structure of the T. thermophilus RNA polymerase elongation complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17581590}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17581590 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17581590}}		{{ABSTRACT_PUBMED_17581590}}

	==About this Structure==		==About this Structure==
-	~~2O5I~~ is a 16 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA].	+	[[2o5i]] is a 16 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O5I OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17581590~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017581590</ref><references group="xtra"/>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
Line 34:		Line 25:
	[[Category: Rna transcript]]		[[Category: Rna transcript]]
	[[Category: Template dna]]		[[Category: Template dna]]
-		+	[[Category: Transferase-dna-rna hybrid complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 23:49:55 2009''~~	+