4nl4 - Revision history

OCA at 12:33, 1 March 2024

OCA — Fri, 01 Mar 2024 12:33:55 GMT

←Older revision		Revision as of 12:33, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nl4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_MGH_78578 Klebsiella pneumoniae subsp. pneumoniae MGH 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NL4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NL4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nl4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_MGH_78578 Klebsiella pneumoniae subsp. pneumoniae MGH 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NL4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NL4 FirstGlance]. <br>
-	</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=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]] 2.65Å</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=ZN:ZINC+ION'>ZN</scene></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=4nl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nl4 OCA], [https://pdbe.org/4nl4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nl4 RCSB], [https://www.ebi.ac.uk/pdbsum/4nl4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nl4 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=4nl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nl4 OCA], [https://pdbe.org/4nl4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nl4 RCSB], [https://www.ebi.ac.uk/pdbsum/4nl4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nl4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A6TGC5_KLEP7 A6TGC5_KLEP7]		[https://www.uniprot.org/uniprot/A6TGC5_KLEP7 A6TGC5_KLEP7]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Collisions between cellular DNA replication machinery (replisomes) and damaged DNA or immovable protein complexes can dissociate replisomes before the completion of replication. This potentially lethal problem is resolved by cellular "replication restart" reactions that recognize the structures of prematurely abandoned replication forks and mediate replisomal reloading. In bacteria, this essential activity is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). However, the mechanisms by which PriA binds replication fork DNA and coordinates subsequent replication restart reactions have remained unclear due to the dearth of high-resolution structural information available for the protein. Here, we describe the crystal structures of full-length PriA and PriA bound to SSB. The structures reveal a modular arrangement for PriA in which several DNA-binding domains surround its helicase core in a manner that appears to be poised for binding to branched replication fork DNA structures while simultaneously allowing complex formation with SSB. PriA interaction with SSB is shown to modulate SSB/DNA complexes in a manner that exposes a potential replication initiation site. From these observations, a model emerges to explain how PriA links recognition of diverse replication forks to replication restart.

-	Structural mechanisms of PriA-mediated DNA replication restart.,Bhattacharyya B, George NP, Thurmes TM, Zhou R, Jani N, Wessel SR, Sandler SJ, Ha T, Keck JL Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1373-8. doi:, 10.1073/pnas.1318001111. Epub 2013 Dec 30. PMID:24379377<ref>PMID:24379377</ref>	+	==See Also==
-		+	*[[Helicase 3D structures\|Helicase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4nl4" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:33, 11 January 2023

OCA — Wed, 11 Jan 2023 08:33:00 GMT

←Older revision		Revision as of 08:33, 11 January 2023
Line 1:		Line 1:

	==PriA Helicase Bound to ADP==		==PriA Helicase Bound to ADP==
-	<StructureSection load='4nl4' size='340' side='right' caption='[[4nl4]], [[Resolution\|resolution]] 2.65Å' scene=''>	+	<StructureSection load='4nl4' size='340' side='right'caption='[[4nl4]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nl4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Klep7 Klep7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NL4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NL4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nl4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._pneumoniae_MGH_78578 Klebsiella pneumoniae subsp. pneumoniae MGH 78578]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NL4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NL4 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=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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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">[[2d7g\|2d7g]], [[2d7h\|2d7h]], [[2dwl\|2dwl]], [[2dwm\|2dwm]], [[2dwn\|2dwn]], [[2d7e\|2d7e]], [[4nl8\|4nl8]]</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=4nl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nl4 OCA], [https://pdbe.org/4nl4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nl4 RCSB], [https://www.ebi.ac.uk/pdbsum/4nl4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nl4 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPN78578_41850, KPN_04230, priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</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=4nl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nl4 OCA], [~~http~~://pdbe.org/4nl4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nl4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nl4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nl4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A6TGC5_KLEP7 A6TGC5_KLEP7]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Klep7~~]]	+	[[Category: Klebsiella pneumoniae subsp. pneumoniae MGH 78578]]
-	[[Category: ~~Bhattacharyya, B~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~George, N P~~]]	+	[[Category: Bhattacharyya B]]
-	[[Category: ~~Keck, J L~~]]	+	[[Category: George NP]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Keck JL]]
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: Pria]]~~	+
-	~~[[Category: Reca]]~~	+
-	~~[[Category: Winged-helix~~]]	+

OCA at 17:30, 9 March 2017

OCA — Thu, 09 Mar 2017 17:30:29 GMT

←Older revision		Revision as of 17:30, 9 March 2017
Line 1:		Line 1:
		+
	==PriA Helicase Bound to ADP==		==PriA Helicase Bound to ADP==
	<StructureSection load='4nl4' size='340' side='right' caption='[[4nl4]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='4nl4' size='340' side='right' caption='[[4nl4]], [[Resolution\|resolution]] 2.65Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d7g\|2d7g]], [[2d7h\|2d7h]], [[2dwl\|2dwl]], [[2dwm\|2dwm]], [[2dwn\|2dwn]], [[2d7e\|2d7e]], [[4nl8\|4nl8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d7g\|2d7g]], [[2d7h\|2d7h]], [[2dwl\|2dwl]], [[2dwm\|2dwm]], [[2dwn\|2dwn]], [[2d7e\|2d7e]], [[4nl8\|4nl8]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPN78578_41850, KPN_04230, priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPN78578_41850, KPN_04230, priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</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=4nl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nl4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nl4 RCSB], [http://www.ebi.ac.uk/pdbsum/4nl4 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=4nl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nl4 OCA], [http://pdbe.org/4nl4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nl4 RCSB], [http://www.ebi.ac.uk/pdbsum/4nl4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nl4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4nl4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:24, 21 December 2014

OCA — Sun, 21 Dec 2014 17:24:57 GMT

←Older revision		Revision as of 17:24, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4nl4\| PDB~~=4nl4 \| ~~SCENE~~= }}	+	==PriA Helicase Bound to ADP==
-	===~~PriA Helicase Bound to~~ ADP===	+	<StructureSection load='4nl4' size='340' side='right' caption='[[4nl4]], [[Resolution\|resolution]] 2.65Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24379377}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4nl4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Klep7 Klep7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NL4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NL4 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=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d7g\|2d7g]], [[2d7h\|2d7h]], [[2dwl\|2dwl]], [[2dwm\|2dwm]], [[2dwn\|2dwn]], [[2d7e\|2d7e]], [[4nl8\|4nl8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPN78578_41850, KPN_04230, priA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272620 KLEP7])</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=4nl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nl4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nl4 RCSB], [http://www.ebi.ac.uk/pdbsum/4nl4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Collisions between cellular DNA replication machinery (replisomes) and damaged DNA or immovable protein complexes can dissociate replisomes before the completion of replication. This potentially lethal problem is resolved by cellular "replication restart" reactions that recognize the structures of prematurely abandoned replication forks and mediate replisomal reloading. In bacteria, this essential activity is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). However, the mechanisms by which PriA binds replication fork DNA and coordinates subsequent replication restart reactions have remained unclear due to the dearth of high-resolution structural information available for the protein. Here, we describe the crystal structures of full-length PriA and PriA bound to SSB. The structures reveal a modular arrangement for PriA in which several DNA-binding domains surround its helicase core in a manner that appears to be poised for binding to branched replication fork DNA structures while simultaneously allowing complex formation with SSB. PriA interaction with SSB is shown to modulate SSB/DNA complexes in a manner that exposes a potential replication initiation site. From these observations, a model emerges to explain how PriA links recognition of diverse replication forks to replication restart.

-	~~==About this Structure==~~	+	Structural mechanisms of PriA-mediated DNA replication restart.,Bhattacharyya B, George NP, Thurmes TM, Zhou R, Jani N, Wessel SR, Sandler SJ, Ha T, Keck JL Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1373-8. doi:, 10.1073/pnas.1318001111. Epub 2013 Dec 30. PMID:24379377<ref>PMID:24379377</ref>
-	~~[[4nl4]] is a 1 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4NL4 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024379377</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Bhattacharyya, B.]]	+	== References ==
-	[[Category: George, N P.]]	+	<references/>
-	[[Category: Keck, J L.]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Klep7]]
		+	[[Category: Bhattacharyya, B]]
		+	[[Category: George, N P]]
		+	[[Category: Keck, J L]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Helicase]]		[[Category: Helicase]]

OCA at 04:16, 13 February 2014

OCA — Thu, 13 Feb 2014 04:16:40 GMT

←Older revision		Revision as of 04:16, 13 February 2014
Line 1:		Line 1:
	{{STRUCTURE_4nl4\| PDB=4nl4 \| SCENE= }}		{{STRUCTURE_4nl4\| PDB=4nl4 \| SCENE= }}
	===PriA Helicase Bound to ADP===		===PriA Helicase Bound to ADP===
		+	{{ABSTRACT_PUBMED_24379377}}

	==About this Structure==		==About this Structure==
	[[4nl4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NL4 OCA].		[[4nl4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NL4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024379377</ref><references group="xtra"/><references/>
	[[Category: Bhattacharyya, B.]]		[[Category: Bhattacharyya, B.]]
	[[Category: George, N P.]]		[[Category: George, N P.]]

OCA at 10:39, 8 January 2014

OCA — Wed, 08 Jan 2014 10:39:06 GMT

←Older revision		Revision as of 10:39, 8 January 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4nl4\| PDB=4nl4 \| SCENE= }}
		+	===PriA Helicase Bound to ADP===

-	~~The entry~~ 4nl4 is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4nl4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NL4 OCA].
-	~~Authors~~: Bhattacharyya, B., George, N.P., Keck, J.L.	+	[[Category: Bhattacharyya, B.]]
-		+	[[Category: George, N P.]]
-	~~Description~~: ~~PriA~~ Helicase ~~Bound to ADP~~	+	[[Category: Keck, J L.]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Helicase]]
		+	[[Category: Pria]]
		+	[[Category: Reca]]
		+	[[Category: Winged-helix]]

OCA: Protected "4nl4" [edit=sysop:move=sysop]

OCA — Wed, 20 Nov 2013 13:01:39 GMT

Protected "4nl4" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:01, 20 November 2013

OCA: New page: '''Unreleased structure''' The entry 4nl4 is ON HOLD Authors: Bhattacharyya, B., George, N.P., Keck, J.L. Description: PriA Helicase Bound to ADP

OCA — Wed, 20 Nov 2013 13:01:39 GMT

New page: '''Unreleased structure''' The entry 4nl4 is ON HOLD Authors: Bhattacharyya, B., George, N.P., Keck, J.L. Description: PriA Helicase Bound to ADP

New page

'''Unreleased structure'''

The entry 4nl4 is ON HOLD

Authors: Bhattacharyya, B., George, N.P., Keck, J.L.

Description: PriA Helicase Bound to ADP