6wq2 - Revision history

OCA at 19:29, 29 May 2024

2024-05-29T19:29:20Z

←Older revision		Revision as of 19:29, 29 May 2024
Line 1:		Line 1:

-	====	+	==Cryo-EM of the S. islandicus filamentous virus, SIFV==
-	<StructureSection load='6wq2' size='340' side='right'caption='[[6wq2]]' scene=''>	+	<StructureSection load='6wq2' size='340' side='right'caption='[[6wq2]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wq2]] is a 36 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_islandicus_filamentous_virus Sulfolobus islandicus filamentous virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WQ2 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=6wq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wq2 OCA], [https://pdbe.org/6wq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wq2 RCSB], [https://www.ebi.ac.uk/pdbsum/6wq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wq2 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]] 4Å</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=6wq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wq2 OCA], [https://pdbe.org/6wq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wq2 RCSB], [https://www.ebi.ac.uk/pdbsum/6wq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wq2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CAPS2_SIFVH CAPS2_SIFVH] Self-assembles to form a helical, filamentous nucleocapsid mesuring 1980 nm in length and 24 nm in width. Together with capsid protein 1, wraps arounds the DNA and maintains it in an A-form. Capsid proteins probably maintain the DNA in A-form by non-specific desolvation and specific coordination of the DNA phosphate groups by positively charged residues. This certainly protects the viral DNA under conditions such as the extreme desiccation of its host.<ref>PMID:32759221</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2.8-A resolution, and Sulfolobus islandicus filamentous virus (SIFV), at 4.0-A resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.
		+
		+	Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments.,Wang F, Baquero DP, Beltran LC, Su Z, Osinski T, Zheng W, Prangishvili D, Krupovic M, Egelman EH Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):19643-19652. doi: , 10.1073/pnas.2011125117. Epub 2020 Aug 5. PMID:32759221<ref>PMID:32759221</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6wq2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z~~-disk~~]]	+	[[Category: Sulfolobus islandicus filamentous virus]]
		+	[[Category: Baquero DP]]
		+	[[Category: Egelman EH]]
		+	[[Category: Krupovic M]]
		+	[[Category: Prangishvili D]]
		+	[[Category: Su Z]]
		+	[[Category: Wang F]]
		+	[[Category: Zheng W]]

OCA at 05:47, 6 October 2021

2021-10-06T05:47:56Z

←Older revision		Revision as of 05:47, 6 October 2021
Line 3:		Line 3:
	<StructureSection load='6wq2' size='340' side='right'caption='[[6wq2]]' scene=''>		<StructureSection load='6wq2' size='340' side='right'caption='[[6wq2]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= 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=6wq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wq2 OCA], [~~http~~://pdbe.org/6wq2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wq2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wq2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wq2 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=6wq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wq2 OCA], [https://pdbe.org/6wq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wq2 RCSB], [https://www.ebi.ac.uk/pdbsum/6wq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wq2 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 11:10, 29 July 2020

2020-07-29T11:10:35Z

←Older revision		Revision as of 11:10, 29 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6wq2 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6wq2' size='340' side='right'caption='[[6wq2]]' scene=''>
-	~~Authors~~: ~~Wang, F~~.~~, Baquero, D~~.P.~~, Su, Z~~.~~, Zheng, W~~.~~, Prangishvili, D~~.~~, Krupovic, M., Egelman, E.H~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Cryo-EM of the S~~. ~~islandicus filamentous virus~~, ~~SIFV~~	+	</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=6wq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wq2 OCA], [http://pdbe.org/6wq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wq2 RCSB], [http://www.ebi.ac.uk/pdbsum/6wq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wq2 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: Su, ~~Z]]~~	+	__TOC__
-	[~~[Category~~: ~~Prangishvili, D~~]]	+	</StructureSection>
-	~~[[Category: Krupovic~~, ~~M]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Baquero, D~~.P]]	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Egelman, E~~.H]]	+
-	[[Category: ~~Wang, F~~]]	+
-	[[Category: ~~Zheng, W~~]]	+

OCA at 04:44, 27 May 2020

2020-05-27T04:44:06Z

←Older revision		Revision as of 04:44, 27 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6wq2 is ON HOLD	+	The entry 6wq2 is ON HOLD until Paper Publication

	Authors: Wang, F., Baquero, D.P., Su, Z., Zheng, W., Prangishvili, D., Krupovic, M., Egelman, E.H.		Authors: Wang, F., Baquero, D.P., Su, Z., Zheng, W., Prangishvili, D., Krupovic, M., Egelman, E.H.
Line 7:		Line 7:
	Description: Cryo-EM of the S. islandicus filamentous virus, SIFV		Description: Cryo-EM of the S. islandicus filamentous virus, SIFV
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Egelman, E.H]]
	[[Category: Su, Z]]		[[Category: Su, Z]]
-	[[Category: Wang, F]]
	[[Category: Prangishvili, D]]		[[Category: Prangishvili, D]]
	[[Category: Krupovic, M]]		[[Category: Krupovic, M]]
	[[Category: Baquero, D.P]]		[[Category: Baquero, D.P]]
		+	[[Category: Egelman, E.H]]
		+	[[Category: Wang, F]]
	[[Category: Zheng, W]]		[[Category: Zheng, W]]

OCA: Protected "6wq2" [edit=sysop:move=sysop]

2020-05-06T04:30:56Z

Protected "6wq2" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:30, 6 May 2020

OCA: New page: '''Unreleased structure''' The entry 6wq2 is ON HOLD Authors: Wang, F., Baquero, D.P., Su, Z., Zheng, W., Prangishvili, D., Krupovic, M., Egelman, E.H. Description: Cryo-EM of the S. i...

2020-05-06T04:30:55Z

New page: '''Unreleased structure''' The entry 6wq2 is ON HOLD Authors: Wang, F., Baquero, D.P., Su, Z., Zheng, W., Prangishvili, D., Krupovic, M., Egelman, E.H. Description: Cryo-EM of the S. i...

New page

'''Unreleased structure'''

The entry 6wq2 is ON HOLD

Authors: Wang, F., Baquero, D.P., Su, Z., Zheng, W., Prangishvili, D., Krupovic, M., Egelman, E.H.

Description: Cryo-EM of the S. islandicus filamentous virus, SIFV
[[Category: Unreleased Structures]]
[[Category: Egelman, E.H]]
[[Category: Su, Z]]
[[Category: Wang, F]]
[[Category: Prangishvili, D]]
[[Category: Krupovic, M]]
[[Category: Baquero, D.P]]
[[Category: Zheng, W]]