5jjk - Revision history

OCA at 18:55, 20 September 2023

2023-09-20T18:55:11Z

←Older revision		Revision as of 18:55, 20 September 2023
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	<StructureSection load='5jjk' size='340' side='right'caption='[[5jjk]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='5jjk' size='340' side='right'caption='[[5jjk]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jjk]] is a 7 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Eco57 Eco57~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JJK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jjk]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] 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=5JJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JJK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.15Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5jji\|5jji]]~~, ~~[[5jjl\|5jjl]]~~<~~/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=5jjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jjk OCA], [https://pdbe.org/5jjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jjk RCSB], [https://www.ebi.ac.uk/pdbsum/5jjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jjk ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">rho, Z5293, ECs4716 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])~~</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=5jjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jjk OCA], [~~http~~://pdbe.org/5jjk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jjk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jjk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jjk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~RHO_ECO57 RHO_ECO57]~~] Facilitates transcription termination by a mechanism that involves ~~Rho~~ binding to the nascent RNA, activation of ~~Rho~~'s RNA-dependent ATPase activity, and release of the mRNA from the DNA template.	+	[https://www.uniprot.org/uniprot/RHO_ECOLI RHO_ECOLI] Facilitates transcription termination by a mechanism that involves rho binding to the nascent RNA, activation of rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. RNA-dependent NTPAse which utilizes all four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01884]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5jjk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jjk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Eco57~~]]	+	[[Category: Escherichia coli O157:H7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Berger, J M~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Lawson, M R~~]]	+	[[Category: Berger JM]]
-	[[Category: ~~Qu, S~~]]	+	[[Category: Lawson MR]]
-	[[Category: ~~Thomsen, N D~~]]	+	[[Category: Qu S]]
-	[[Category: ~~Witkowsky, L B~~]]	+	[[Category: Thomsen ND]]
-	[[Category: ~~Protein-rna complex]]~~	+	[[Category: Witkowsky LB]]
-	~~[[Category: Transcription-rna complex~~]]	+

OCA at 12:02, 25 December 2019

2019-12-25T12:02:46Z

←Older revision		Revision as of 12:02, 25 December 2019
Line 1:		Line 1:

	==Rho transcription termination factor bound to rA7 and 6 ADP-BeF3 molecules==		==Rho transcription termination factor bound to rA7 and 6 ADP-BeF3 molecules==
-	<StructureSection load='5jjk' size='340' side='right' caption='[[5jjk]], [[Resolution\|resolution]] 3.15Å' scene=''>	+	<StructureSection load='5jjk' size='340' side='right'caption='[[5jjk]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jjk]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jjk]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JJK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jji\|5jji]], [[5jjl\|5jjl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jji\|5jji]], [[5jjl\|5jjl]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rho, Z5293, ECs4716 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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=5jjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jjk OCA], [http://pdbe.org/5jjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jjk RCSB], [http://www.ebi.ac.uk/pdbsum/5jjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jjk ProSAT]</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=5jjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jjk OCA], [http://pdbe.org/5jjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jjk RCSB], [http://www.ebi.ac.uk/pdbsum/5jjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jjk ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Eco57]]
		+	[[Category: Large Structures]]
	[[Category: Berger, J M]]		[[Category: Berger, J M]]
	[[Category: Lawson, M R]]		[[Category: Lawson, M R]]

OCA at 09:46, 2 January 2017

2017-01-02T09:46:19Z

←Older revision		Revision as of 09:46, 2 January 2017
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RHO_ECO57 RHO_ECO57]] Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template.		[[http://www.uniprot.org/uniprot/RHO_ECO57 RHO_ECO57]] Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ring-shaped hexameric helicases and translocases support essential DNA-, RNA-, and protein-dependent transactions in all cells and many viruses. How such systems coordinate ATPase activity between multiple subunits to power conformational changes that drive the engagement and movement of client substrates is a fundamental question. Using the Escherichia coli Rho transcription termination factor as a model system, we have used solution and crystallographic structural methods to delineate the range of conformational changes that accompany distinct substrate and nucleotide cofactor binding events. Small-angle X-ray scattering data show that Rho preferentially adopts an open-ring state in solution and that RNA and ATP are both required to cooperatively promote ring closure. Multiple closed-ring structures with different RNA substrates and nucleotide occupancies capture distinct catalytic intermediates accessed during translocation. Our data reveal how RNA-induced ring closure templates a sequential ATP-hydrolysis mechanism, provide a molecular rationale for how the Rho ATPase domains distinguishes between distinct RNA sequences, and establish structural snapshots of substepping events in a hexameric helicase/translocase.
		+
		+	Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.,Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7691-E7700. Epub 2016 Nov 16. PMID:27856760<ref>PMID:27856760</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jjk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:59, 22 December 2016

2016-12-22T14:59:27Z

←Older revision		Revision as of 14:59, 22 December 2016
Line 1:		Line 1:

-	==~~Protein/nucleic acid complex 2~~==	+	==Rho transcription termination factor bound to rA7 and 6 ADP-BeF3 molecules==
	<StructureSection load='5jjk' size='340' side='right' caption='[[5jjk]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='5jjk' size='340' side='right' caption='[[5jjk]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 03:27, 10 December 2016

2016-12-10T03:27:33Z

←Older revision		Revision as of 03:27, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jjk is ~~ON HOLD until Paper Publication~~	+	==Protein/nucleic acid complex 2==
-		+	<StructureSection load='5jjk' size='340' side='right' caption='[[5jjk]], [[Resolution\|resolution]] 3.15Å' scene=''>
-	~~Authors~~: ~~Thomsen~~, N.D., ~~Lawson, M~~.R., ~~Witkowsky~~, L.B., ~~Qu, S~~., ~~Berger, J~~.M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jjk]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JJK FirstGlance]. <br>
-	~~Description: Protein~~/~~nucleic acid complex 2~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[Category: Berger, J.M]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jji\|5jji]], [[5jjl\|5jjl]]</td></tr>
-	[[Category: ~~Thomsen~~, ~~N.D~~]]	+	<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=5jjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jjk OCA], [http://pdbe.org/5jjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jjk RCSB], [http://www.ebi.ac.uk/pdbsum/5jjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jjk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RHO_ECO57 RHO_ECO57]] Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Berger, J M]]
		+	[[Category: Lawson, M R]]
	[[Category: Qu, S]]		[[Category: Qu, S]]
-	[[Category: Witkowsky, L.B]]	+	[[Category: Thomsen, N D]]
-	[[Category: ~~Lawson, M.R~~]]	+	[[Category: Witkowsky, L B]]
		+	[[Category: Protein-rna complex]]
		+	[[Category: Transcription-rna complex]]

OCA at 12:49, 20 June 2016

2016-06-20T12:49:29Z

←Older revision		Revision as of 12:49, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jjk is ON HOLD	+	The entry 5jjk is ON HOLD until Paper Publication

	Authors: Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M.		Authors: Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M.

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

2016-05-11T02:10:30Z

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

←Older revision

Revision as of 02:10, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jjk is ON HOLD Authors: Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M. Description: Protein/nucleic acid complex 2 [[Category:...

2016-05-11T02:10:29Z

New page: '''Unreleased structure''' The entry 5jjk is ON HOLD Authors: Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M. Description: Protein/nucleic acid complex 2 [[Category:...

New page

'''Unreleased structure'''

The entry 5jjk is ON HOLD

Authors: Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M.

Description: Protein/nucleic acid complex 2
[[Category: Unreleased Structures]]
[[Category: Berger, J.M]]
[[Category: Thomsen, N.D]]
[[Category: Qu, S]]
[[Category: Witkowsky, L.B]]
[[Category: Lawson, M.R]]