4idh - Revision history

OCA at 11:53, 1 March 2024

2024-03-01T11:53:27Z

←Older revision		Revision as of 11:53, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IDH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IDH FirstGlance]. <br>
-	</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=4idh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4idh OCA], [https://pdbe.org/4idh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4idh RCSB], [https://www.ebi.ac.uk/pdbsum/4idh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4idh ProSAT]</span></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]] 1.69Å</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=4idh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4idh OCA], [https://pdbe.org/4idh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4idh RCSB], [https://www.ebi.ac.uk/pdbsum/4idh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4idh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q716H3_BPSFV Q716H3_BPSFV]		[https://www.uniprot.org/uniprot/Q716H3_BPSFV Q716H3_BPSFV]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Many DNA viruses use powerful molecular motors to cleave concatemeric viral DNA into genome-length units and package them into preformed procapsid powered by ATP hydrolysis. Here we report the structures of the DNA-packaging motor gp2 of bacteriophage Sf6, which reveal a unique clade of RecA-like ATPase domain and an RNase H-like nuclease domain tethered by a regulatory linker domain, exhibiting a strikingly distinct domain arrangement. The gp2 structures complexed with nucleotides reveal, at the atomic detail, the catalytic center embraced by the ATPase domain and the linker domain. The gp2 nuclease activity is modulated by the ATPase domain and is stimulated by ATP. An extended DNA-binding surface is formed by the linker domain and the nuclease domain. These results suggest a unique mechanism for translation of chemical reaction into physical motion of DNA and provide insights into coordination of DNA translocation and cleavage in a viral DNA-packaging motor, which may be achieved via linker-domain-mediated interdomain communication driven by ATP hydrolysis.
-
-	Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage.,Zhao H, Christensen TE, Kamau YN, Tang L Proc Natl Acad Sci U S A. 2013 May 14;110(20):8075-8080. Epub 2013 Apr 29. PMID:23630261<ref>PMID:23630261</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4idh" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Terminase 3D Structures\|Terminase 3D Structures]]		*[[Terminase 3D Structures\|Terminase 3D Structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:02, 9 November 2022

2022-11-09T09:02:49Z

←Older revision		Revision as of 09:02, 9 November 2022
Line 3:		Line 3:
	<StructureSection load='4idh' size='340' side='right'caption='[[4idh]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='4idh' size='340' side='right'caption='[[4idh]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpsfv Bpsfv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IDH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IDH FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iee\|4iee]], [[4iei\|4iei]], [[4ife\|4ife]]</td></tr>~~	+	</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=4idh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4idh OCA], [https://pdbe.org/4idh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4idh RCSB], [https://www.ebi.ac.uk/pdbsum/4idh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4idh 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=4idh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4idh OCA], [~~http~~://pdbe.org/4idh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4idh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4idh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4idh ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q716H3_BPSFV Q716H3_BPSFV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:

	==See Also==		==See Also==
-	*[[Terminase\|Terminase]]	+	*[[Terminase 3D Structures\|Terminase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bpsfv]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Christensen, T]]	+	[[Category: Shigella virus Sf6]]
-	[[Category: Kamau, Y]]	+	[[Category: Christensen T]]
-	[[Category: Tang, L]]	+	[[Category: Kamau Y]]
-	[[Category: Zhao, H]]	+	[[Category: Tang L]]
-	~~[[Category: Atp binding]]~~	+	[[Category: Zhao H]]
-	~~[[Category: Atpase]]~~	+
-	~~[[Category: Dna packaging]]~~	+
-	~~[[Category: Magnesium binding]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Terminase]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 05:25, 13 February 2020

2020-02-13T05:25:55Z

←Older revision		Revision as of 05:25, 13 February 2020
Line 1:		Line 1:

	==Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6==		==Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6==
-	<StructureSection load='4idh' size='340' side='right' caption='[[4idh]], [[Resolution\|resolution]] 1.69Å' scene=''>	+	<StructureSection load='4idh' size='340' side='right'caption='[[4idh]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpsfv Bpsfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IDH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpsfv Bpsfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IDH FirstGlance]. <br>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4idh" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4idh" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Terminase\|Terminase]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Bpsfv]]		[[Category: Bpsfv]]
		+	[[Category: Large Structures]]
	[[Category: Christensen, T]]		[[Category: Christensen, T]]
	[[Category: Kamau, Y]]		[[Category: Kamau, Y]]

OCA at 13:00, 4 August 2016

2016-08-04T13:00:16Z

←Older revision		Revision as of 13:00, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6==		==Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6==
	<StructureSection load='4idh' size='340' side='right' caption='[[4idh]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='4idh' size='340' side='right' caption='[[4idh]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Shigella_phage_sf6 Shigella phage sf6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IDH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpsfv Bpsfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IDH FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iee\|4iee]], [[4iei\|4iei]], [[4ife\|4ife]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iee\|4iee]], [[4iei\|4iei]], [[4ife\|4ife]]</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=4idh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4idh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4idh RCSB], [http://www.ebi.ac.uk/pdbsum/4idh 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=4idh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4idh OCA], [http://pdbe.org/4idh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4idh RCSB], [http://www.ebi.ac.uk/pdbsum/4idh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4idh ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4idh" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Shigella phage sf6~~]]	+	[[Category: Bpsfv]]
	[[Category: Christensen, T]]		[[Category: Christensen, T]]
	[[Category: Kamau, Y]]		[[Category: Kamau, Y]]

OCA at 12:59, 21 December 2014

2014-12-21T12:59:17Z

←Older revision		Revision as of 12:59, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4idh\| PDB=4idh \| SCENE= }}~~	+	==Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6==
-	===Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6===	+	<StructureSection load='4idh' size='340' side='right' caption='[[4idh]], [[Resolution\|resolution]] 1.69Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23630261}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4idh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_phage_sf6 Shigella phage sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IDH FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iee\|4iee]], [[4iei\|4iei]], [[4ife\|4ife]]</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=4idh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4idh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4idh RCSB], [http://www.ebi.ac.uk/pdbsum/4idh PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many DNA viruses use powerful molecular motors to cleave concatemeric viral DNA into genome-length units and package them into preformed procapsid powered by ATP hydrolysis. Here we report the structures of the DNA-packaging motor gp2 of bacteriophage Sf6, which reveal a unique clade of RecA-like ATPase domain and an RNase H-like nuclease domain tethered by a regulatory linker domain, exhibiting a strikingly distinct domain arrangement. The gp2 structures complexed with nucleotides reveal, at the atomic detail, the catalytic center embraced by the ATPase domain and the linker domain. The gp2 nuclease activity is modulated by the ATPase domain and is stimulated by ATP. An extended DNA-binding surface is formed by the linker domain and the nuclease domain. These results suggest a unique mechanism for translation of chemical reaction into physical motion of DNA and provide insights into coordination of DNA translocation and cleavage in a viral DNA-packaging motor, which may be achieved via linker-domain-mediated interdomain communication driven by ATP hydrolysis.

-	~~==About this Structure==~~	+	Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage.,Zhao H, Christensen TE, Kamau YN, Tang L Proc Natl Acad Sci U S A. 2013 May 14;110(20):8075-8080. Epub 2013 Apr 29. PMID:23630261<ref>PMID:23630261</ref>
-	~~[[4idh]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Shigella_phage_sf6 Shigella phage sf6]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4IDH OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023630261</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Shigella phage sf6]]		[[Category: Shigella phage sf6]]
-	[[Category: Christensen, T.]]	+	[[Category: Christensen, T]]
-	[[Category: Kamau, Y.]]	+	[[Category: Kamau, Y]]
-	[[Category: Tang, L.]]	+	[[Category: Tang, L]]
-	[[Category: Zhao, H.]]	+	[[Category: Zhao, H]]
	[[Category: Atp binding]]		[[Category: Atp binding]]
	[[Category: Atpase]]		[[Category: Atpase]]

OCA at 16:32, 19 June 2013

2013-06-19T16:32:52Z

←Older revision		Revision as of 16:32, 19 June 2013
Line 5:		Line 5:
	==About this Structure==		==About this Structure==
	[[4idh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_phage_sf6 Shigella phage sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA].		[[4idh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_phage_sf6 Shigella phage sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023630261</ref><references group="xtra"/><references/>
	[[Category: Shigella phage sf6]]		[[Category: Shigella phage sf6]]
	[[Category: Christensen, T.]]		[[Category: Christensen, T.]]

OCA at 06:04, 16 May 2013

2013-05-16T06:04:48Z

←Older revision		Revision as of 06:04, 16 May 2013
Line 1:		Line 1:
	{{STRUCTURE_4idh\| PDB=4idh \| SCENE= }}		{{STRUCTURE_4idh\| PDB=4idh \| SCENE= }}
	===Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6===		===Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6===
		+	{{ABSTRACT_PUBMED_23630261}}

	==About this Structure==		==About this Structure==

OCA at 07:51, 2 May 2013

2013-05-02T07:51:52Z

←Older revision		Revision as of 07:51, 2 May 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4idh\| PDB=4idh \| SCENE= }}
		+	===Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6===

-	~~The entry~~ 4idh is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4idh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shigella_phage_sf6 Shigella phage sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IDH OCA].
-	~~Authors~~: ~~Zhao, H.,~~ Christensen, T., Kamau, Y., Tang, L.	+	[[Category: Shigella phage sf6]]
-		+	[[Category: Christensen, T.]]
-	~~Description~~: ~~Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6~~	+	[[Category: Kamau, Y.]]
		+	[[Category: Tang, L.]]
		+	[[Category: Zhao, H.]]
		+	[[Category: Atp binding]]
		+	[[Category: Atpase]]
		+	[[Category: Dna packaging]]
		+	[[Category: Magnesium binding]]
		+	[[Category: Nuclease]]
		+	[[Category: Terminase]]
		+	[[Category: Viral protein]]

OCA at 11:09, 23 January 2013

2013-01-23T11:09:38Z

←Older revision		Revision as of 11:09, 23 January 2013
Line 3:		Line 3:
	The entry 4idh is ON HOLD		The entry 4idh is ON HOLD

-	Authors: Zhao, H., Christensen, T., Kamau, Y. , Tang, L.	+	Authors: Zhao, H., Christensen, T., Kamau, Y., Tang, L.

	Description: Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6		Description: Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6

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

2012-12-19T11:08:14Z

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

←Older revision

Revision as of 11:08, 19 December 2012