3j26 - Revision history

OCA at 10:09, 21 February 2024

OCA — Wed, 21 Feb 2024 10:09:42 GMT

←Older revision		Revision as of 10:09, 21 February 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CAPSD_SPTNK CAPSD_SPTNK]		[https://www.uniprot.org/uniprot/CAPSD_SPTNK CAPSD_SPTNK]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	"Sputnik" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-A resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double "jelly-roll" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.
-
-	Structure of Sputnik, a virophage, at 3.5-A resolution.,Zhang X, Sun S, Xiang Y, Wong J, Klose T, Raoult D, Rossmann MG Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18431-6. doi:, 10.1073/pnas.1211702109. Epub 2012 Oct 22. PMID:23091035<ref>PMID:23091035</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3j26" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>

OCA at 14:13, 24 January 2024

OCA — Wed, 24 Jan 2024 14:13:49 GMT

←Older revision		Revision as of 14:13, 24 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J26 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J26 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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [https://pdbe.org/3j26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [https://www.ebi.ac.uk/pdbsum/3j26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j26 ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.5Å</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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [https://pdbe.org/3j26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [https://www.ebi.ac.uk/pdbsum/3j26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j26 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CAPSD_SPTNK CAPSD_SPTNK]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 24:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Sputnik virophage]]		[[Category: Sputnik virophage]]
-	[[Category: Zhang~~, X Z]]~~	+	[[Category: Zhang XZ]]
-	~~[[Category: Double jelly-roll]]~~	+
-	~~[[Category: Single jelly-roll]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 03:48, 21 April 2022

OCA — Thu, 21 Apr 2022 03:48:11 GMT

←Older revision		Revision as of 03:48, 21 April 2022
Line 3:		Line 3:
	<SX load='3j26' size='340' side='right' viewer='molstar' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>		<SX load='3j26' size='340' side='right' viewer='molstar' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3J26 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J26 FirstGlance]. <br>
-	</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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [~~http~~://pdbe.org/3j26 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3j26 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3j26 ProSAT]</span></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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [https://pdbe.org/3j26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [https://www.ebi.ac.uk/pdbsum/3j26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j26 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:45, 10 April 2020

OCA — Fri, 10 Apr 2020 17:45:19 GMT

←Older revision		Revision as of 17:45, 10 April 2020
Line 3:		Line 3:
	<SX load='3j26' size='340' side='right' viewer='molstar' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>		<SX load='3j26' size='340' side='right' viewer='molstar' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3J26 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J26 FirstGlance]. <br>
-	</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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [http://pdbe.org/3j26 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [http://www.ebi.ac.uk/pdbsum/3j26 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j26 ProSAT]</span></td></tr>	+	</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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [http://pdbe.org/3j26 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [http://www.ebi.ac.uk/pdbsum/3j26 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j26 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:26, 5 March 2020

OCA — Thu, 05 Mar 2020 04:26:45 GMT

←Older revision		Revision as of 04:26, 5 March 2020
Line 1:		Line 1:

	==The 3.5 A resolution structure of the Sputnik virophage by cryo-EM==		==The 3.5 A resolution structure of the Sputnik virophage by cryo-EM==
-	<~~StructureSection~~ load='3j26' size='340' side='right' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<SX load='3j26' size='340' side='right' viewer='molstar' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J26 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J26 FirstGlance]. <br>
Line 18:		Line 18:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
		+	[[Category: Large Structures]]
	[[Category: Sputnik virophage]]		[[Category: Sputnik virophage]]
	[[Category: Zhang, X Z]]		[[Category: Zhang, X Z]]

OCA at 07:41, 5 August 2016

OCA — Fri, 05 Aug 2016 07:41:04 GMT

←Older revision		Revision as of 07:41, 5 August 2016
Line 1:		Line 1:
		+
	==The 3.5 A resolution structure of the Sputnik virophage by cryo-EM==		==The 3.5 A resolution structure of the Sputnik virophage by cryo-EM==
	<StructureSection load='3j26' size='340' side='right' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='3j26' size='340' side='right' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J26 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J26 FirstGlance]. <br>
-	</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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [http://www.ebi.ac.uk/pdbsum/3j26 PDBsum]</span></td></tr>	+	</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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [http://pdbe.org/3j26 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [http://www.ebi.ac.uk/pdbsum/3j26 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j26 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 14:
	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 3j26" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:55, 18 December 2014

OCA — Thu, 18 Dec 2014 17:55:15 GMT

←Older revision		Revision as of 17:55, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3j26\| PDB=3j26 \| SCENE= }}~~	+	==The 3.5 A resolution structure of the Sputnik virophage by cryo-EM==
-	===The 3.5 A resolution structure of the Sputnik virophage by cryo-EM===	+	<StructureSection load='3j26' size='340' side='right' caption='[[3j26]], [[Resolution\|resolution]] 3.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23091035}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J26 FirstGlance]. <br>
		+	</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=3j26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j26 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j26 RCSB], [http://www.ebi.ac.uk/pdbsum/3j26 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	"Sputnik" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-A resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double "jelly-roll" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.

-	~~==About this~~ Structure==	+	Structure of Sputnik, a virophage, at 3.5-A resolution.,Zhang X, Sun S, Xiang Y, Wong J, Klose T, Raoult D, Rossmann MG Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18431-6. doi:, 10.1073/pnas.1211702109. Epub 2012 Oct 22. PMID:23091035<ref>PMID:23091035</ref>
-	~~[[3j26]] is~~ a ~~14 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sputnik_virophage Sputnik virophage]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3J26 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023091035</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Sputnik virophage]]		[[Category: Sputnik virophage]]
-	[[Category: Zhang, X Z.]]	+	[[Category: Zhang, X Z]]
	[[Category: Double jelly-roll]]		[[Category: Double jelly-roll]]
	[[Category: Single jelly-roll]]		[[Category: Single jelly-roll]]
	[[Category: Virus]]		[[Category: Virus]]

OCA at 04:32, 18 July 2013

OCA — Thu, 18 Jul 2013 04:32:14 GMT

←Older revision		Revision as of 04:32, 18 July 2013
Line 1:		Line 1:
-	[[Image:3j26.png\|left\|200px]]
-
	{{STRUCTURE_3j26\| PDB=3j26 \| SCENE= }}		{{STRUCTURE_3j26\| PDB=3j26 \| SCENE= }}
-
	===The 3.5 A resolution structure of the Sputnik virophage by cryo-EM===		===The 3.5 A resolution structure of the Sputnik virophage by cryo-EM===
-
	{{ABSTRACT_PUBMED_23091035}}		{{ABSTRACT_PUBMED_23091035}}

	==About this Structure==		==About this Structure==
	[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA].		[[3j26]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Sputnik_virophage Sputnik virophage]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J26 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023091035</ref><references group="xtra"/><references/>
	[[Category: Sputnik virophage]]		[[Category: Sputnik virophage]]
	[[Category: Zhang, X Z.]]		[[Category: Zhang, X Z.]]

OCA at 10:33, 14 November 2012

OCA — Wed, 14 Nov 2012 10:33:47 GMT

←Older revision		Revision as of 10:33, 14 November 2012
Line 5:		Line 5:
	===The 3.5 A resolution structure of the Sputnik virophage by cryo-EM===		===The 3.5 A resolution structure of the Sputnik virophage by cryo-EM===

		+	{{ABSTRACT_PUBMED_23091035}}

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

OCA at 07:05, 14 November 2012

OCA — Wed, 14 Nov 2012 07:05:03 GMT

←Older revision		Revision as of 07:05, 14 November 2012
Line 5:		Line 5:
	===The 3.5 A resolution structure of the Sputnik virophage by cryo-EM===		===The 3.5 A resolution structure of the Sputnik virophage by cryo-EM===

-	{{ABSTRACT_PUBMED_23091035}}

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