3e2e - Revision history

OCA at 09:44, 21 February 2024

2024-02-21T09:44:07Z

←Older revision		Revision as of 09:44, 21 February 2024
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	<StructureSection load='3e2e' size='340' side='right'caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3e2e' size='340' side='right'caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpt7 Bpt7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E2E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E2E FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[3e3j\|3e3j]]</div></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~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10760 BPT7])</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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [https://pdbe.org/3e2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [https://www.ebi.ac.uk/pdbsum/3e2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2e 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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [https://pdbe.org/3e2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [https://www.ebi.ac.uk/pdbsum/3e2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.	+	[https://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3e2e 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=3e2e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Structural studies of the T7 bacteriophage DNA-dependent RNA polymerase (T7 RNAP) have shown that the conformation of the amino-terminal domain changes substantially between the initiation and elongation phases of transcription, but how this transition is achieved remains unclear. We report crystal structures of T7 RNAP bound to promoter DNA containing either a 7- or an 8-nucleotide (nt) RNA transcript that illuminate intermediate states along the transition pathway. The amino-terminal domain comprises the C-helix subdomain and the promoter binding domain (PBD), which consists of two segments separated by subdomain H. The structures of the intermediate complex reveal that the PBD and the bound promoter rotate by approximately 45 degrees upon synthesis of an 8-nt RNA transcript. This allows the promoter contacts to be maintained while the active site is expanded to accommodate a growing heteroduplex. The C-helix subdomain moves modestly toward its elongation conformation, whereas subdomain H remains in its initiation- rather than its elongation-phase location, more than 70 angstroms away.
-
-	The structure of a transcribing t7 RNA polymerase in transition from initiation to elongation.,Durniak KJ, Bailey S, Steitz TA Science. 2008 Oct 24;322(5901):553-7. PMID:18948533<ref>PMID:18948533</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3e2e" 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: ~~Bpt7]]~~	+	[[Category: Escherichia phage T7]]
-	~~[[Category: DNA-directed RNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bailey, S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Durniak, K J~~]]	+	[[Category: Bailey S]]
-	[[Category: ~~Steitz, T A~~]]	+	[[Category: Durniak KJ]]
-	[[Category: ~~Dna-directed rna polymerase]]~~	+	[[Category: Steitz TA]]
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: T7 rna polymerase]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-rna-dna complex~~]]	+

OCA at 19:33, 20 October 2021

2021-10-20T19:33:33Z

←Older revision		Revision as of 19:33, 20 October 2021
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	<StructureSection load='3e2e' size='340' side='right'caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3e2e' size='340' side='right'caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3E2E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E2E FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e3j\|3e3j]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e3j\|3e3j]]</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [~~http~~://pdbe.org/3e2e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3e2e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2e ProSAT]</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'>[https://proteopedia.org/fgij/fg.htm?mol=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [https://pdbe.org/3e2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [https://www.ebi.ac.uk/pdbsum/3e2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.	+	[[https://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 32:

	==See Also==		==See Also==
-	*[[Molecular Playground/T7 RNA Polymerase (7 mer int)\|Molecular Playground/T7 RNA Polymerase (7 mer int)]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	*[[RNA polymerase\|RNA polymerase]]	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpt7]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:25, 31 July 2019

2019-07-31T07:25:01Z

←Older revision		Revision as of 07:25, 31 July 2019
Line 1:		Line 1:

	==Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA==		==Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA==
-	<StructureSection load='3e2e' size='340' side='right' caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='3e2e' size='340' side='right'caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2E FirstGlance]. <br>		<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2E FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/3e2e_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/3e2e_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>
Line 32:		Line 32:
	==See Also==		==See Also==
	*[[Molecular Playground/T7 RNA Polymerase (7 mer int)\|Molecular Playground/T7 RNA Polymerase (7 mer int)]]		*[[Molecular Playground/T7 RNA Polymerase (7 mer int)\|Molecular Playground/T7 RNA Polymerase (7 mer int)]]
		+	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Bailey, S]]		[[Category: Bailey, S]]
	[[Category: Durniak, K J]]		[[Category: Durniak, K J]]

OCA at 09:00, 25 October 2017

2017-10-25T09:00:58Z

←Older revision		Revision as of 09:00, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA==		==Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA==
	<StructureSection load='3e2e' size='340' side='right' caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3e2e' size='340' side='right' caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2E FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e3j\|3e3j]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e3j\|3e3j]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T7])</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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [http://pdbe.org/3e2e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [http://www.ebi.ac.uk/pdbsum/3e2e 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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [http://pdbe.org/3e2e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [http://www.ebi.ac.uk/pdbsum/3e2e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:
	==See Also==		==See Also==
	*[[Molecular Playground/T7 RNA Polymerase (7 mer int)\|Molecular Playground/T7 RNA Polymerase (7 mer int)]]		*[[Molecular Playground/T7 RNA Polymerase (7 mer int)\|Molecular Playground/T7 RNA Polymerase (7 mer int)]]
-	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacteriophage t7]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Bailey, S]]		[[Category: Bailey, S]]

OCA at 18:18, 7 February 2016

2016-02-07T18:18:55Z

←Older revision		Revision as of 18:18, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3e2e' size='340' side='right' caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3e2e' size='340' side='right' caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t7 Enterobacteria phage~~ t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2E FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e3j\|3e3j]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e3j\|3e3j]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~10760 Enterobacteria phage~~ T7])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T7])</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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [http://www.ebi.ac.uk/pdbsum/3e2e 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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [http://pdbe.org/3e2e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [http://www.ebi.ac.uk/pdbsum/3e2e PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3e2e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3e2e" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteriophage t7]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
-	[[Category: Enterobacteria phage t7]]
	[[Category: Bailey, S]]		[[Category: Bailey, S]]
	[[Category: Durniak, K J]]		[[Category: Durniak, K J]]

OCA at 17:22, 24 December 2014

2014-12-24T17:22:48Z

←Older revision		Revision as of 17:22, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3e2e\| PDB=3e2e \| SCENE= }}~~	+	==Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA==
-	===Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA===	+	<StructureSection load='3e2e' size='340' side='right' caption='[[3e2e]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18948533}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3e2e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2E FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e3j\|3e3j]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7])</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=3e2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e2e RCSB], [http://www.ebi.ac.uk/pdbsum/3e2e PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
		+	== 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/e2/3e2e_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 ==
		+	Structural studies of the T7 bacteriophage DNA-dependent RNA polymerase (T7 RNAP) have shown that the conformation of the amino-terminal domain changes substantially between the initiation and elongation phases of transcription, but how this transition is achieved remains unclear. We report crystal structures of T7 RNAP bound to promoter DNA containing either a 7- or an 8-nucleotide (nt) RNA transcript that illuminate intermediate states along the transition pathway. The amino-terminal domain comprises the C-helix subdomain and the promoter binding domain (PBD), which consists of two segments separated by subdomain H. The structures of the intermediate complex reveal that the PBD and the bound promoter rotate by approximately 45 degrees upon synthesis of an 8-nt RNA transcript. This allows the promoter contacts to be maintained while the active site is expanded to accommodate a growing heteroduplex. The C-helix subdomain moves modestly toward its elongation conformation, whereas subdomain H remains in its initiation- rather than its elongation-phase location, more than 70 angstroms away.

-	~~==About this Structure==~~	+	The structure of a transcribing t7 RNA polymerase in transition from initiation to elongation.,Durniak KJ, Bailey S, Steitz TA Science. 2008 Oct 24;322(5901):553-7. PMID:18948533<ref>PMID:18948533</ref>
-	~~[[3e2e]] is~~ a ~~4 chain structure with sequence~~ from ~~[http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3E2E OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Molecular Playground/T7 RNA Polymerase (7 mer int)\|Molecular Playground/T7 RNA Polymerase (7 mer int)]]		*[[Molecular Playground/T7 RNA Polymerase (7 mer int)\|Molecular Playground/T7 RNA Polymerase (7 mer int)]]
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018948533<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Enterobacteria phage t7]]		[[Category: Enterobacteria phage t7]]
-	[[Category: Bailey, S.]]	+	[[Category: Bailey, S]]
-	[[Category: Durniak, K J.]]	+	[[Category: Durniak, K J]]
-	[[Category: Steitz, T A.]]	+	[[Category: Steitz, T A]]
	[[Category: Dna-directed rna polymerase]]		[[Category: Dna-directed rna polymerase]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]

OCA at 09:14, 11 March 2013

2013-03-11T09:14:02Z

←Older revision		Revision as of 09:14, 11 March 2013
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-	[[Image:3e2e.png\|left\|200px]]
-
	{{STRUCTURE_3e2e\| PDB=3e2e \| SCENE= }}		{{STRUCTURE_3e2e\| PDB=3e2e \| SCENE= }}
-
	===Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA===		===Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA===
-
	{{ABSTRACT_PUBMED_18948533}}		{{ABSTRACT_PUBMED_18948533}}

OCA at 07:30, 20 October 2012

2012-10-20T07:30:07Z

←Older revision		Revision as of 07:30, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3e2e]] is a 4 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA].	+	[[3e2e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA].

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

OCA at 16:31, 25 July 2012

2012-07-25T16:31:41Z

←Older revision		Revision as of 16:31, 25 July 2012
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	[[Image:3e2e.png\|left\|200px]]		[[Image:3e2e.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3e2e", 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_3e2e\| PDB=3e2e \| SCENE= }}		{{STRUCTURE_3e2e\| PDB=3e2e \| SCENE= }}

	===Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA===		===Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18948533}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18948533 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18948533}}		{{ABSTRACT_PUBMED_18948533}}

	==About this Structure==		==About this Structure==
-	[[3e2e]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA].	+	[[3e2e]] is a 4 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2E OCA].

	==See Also==		==See Also==
-	*[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]	+	*[[Molecular Playground/T7 RNA Polymerase (7 mer int)\|Molecular Playground/T7 RNA Polymerase (7 mer int)]]
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18948533~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018948533</ref><references group="xtra"/>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Enterobacteria phage t7]]		[[Category: Enterobacteria phage t7]]
Line 36:		Line 26:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: Transferase/rna/dna complex]]	+	[[Category: Transferase-rna-dna complex]]

OCA: Protected "3e2e" [edit=sysop:move=sysop]

2010-12-28T13:19:49Z

Protected "3e2e" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:19, 28 December 2010