3j9a - Revision history

OCA: Redirecting to 6cgr

OCA — Wed, 14 Mar 2018 06:13:48 GMT

Redirecting to 6cgr

←Older revision		Revision as of 06:13, 14 March 2018
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-		+	#REDIRECT [[6cgr]] This PDB entry is obsolete and replaced by 6cgr
-	~~==Backbone model of the smallest capsid protein (SCP) of Kaposi's sarcoma-associated herpesvirus (KSHV)==~~	+
-	~~<StructureSection load='3j9a' size='340' side='right' caption='~~[[~~3j9a]], [[Resolution\|resolution]] 6.00Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[3j9a~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9A 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=3j9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9a OCA], [http://pdbe.org/3j9a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j9a RCSB], [http://www.ebi.ac.uk/pdbsum/3j9a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9a ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Function ==~~	+
-	~~[[http://www.uniprot.org/uniprot/VP26_HHV8P VP26_HHV8P]] Participates in the assembly of the infectious particles by decorating the outer surface of the capsid shell~~ and thus forming a layer between the capsid and the tegument. Complexes composed of the major capsid protein ORF25 and VP26 assemble together in the host cytoplasm and are translocated to the nucleus, where they accumulate and participate in capsid assembly (By similarity).	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	With just one eighth the size of the major capsid protein (MCP), the smallest capsid protein (SCP) of human tumor herpesviruses-Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV)-is vital to capsid assembly, yet its mechanism of action is unknown. Here, by cryoEM of KSHV at 6-A resolution, we show that SCP forms a crown on each hexon and uses a kinked helix to cross-link neighboring MCP subunits. SCP-null mutation decreased viral titer by 1,000 times and impaired but did not fully abolish capsid assembly, indicating an important but nonessential role of SCP. By truncating the C-terminal half of SCP and performing cryoEM reconstruction, we demonstrate that SCP's N-terminal half is responsible for the observed structure and function whereas the C-terminal half is flexible and dispensable. Serial truncations further highlight the critical importance of the N-terminal 10 aa, and cryoEM reconstruction of the one with six residues truncated localizes the N terminus of SCP in the cryoEM density map and enables us to construct a pseudoatomic model of SCP. Fitting of this SCP model and a homology model for the MCP upper domain into the cryoEM map reveals that SCP binds MCP largely via hydrophobic interactions and the kinked helix of SCP bridges over neighboring MCPs to form noncovalent cross-links. These data support a mechanistic model that tumor herpesvirus SCP reinforces the capsid for genome packaging, thus acting as a cementing protein similar to those found in many bacteriophages.	+
-		+
-	CryoEM and mutagenesis reveal that the smallest capsid protein cements and stabilizes Kaposi's sarcoma-associated herpesvirus capsid.,Dai X, Gong D, Xiao Y, Wu TT, Sun R, Zhou ZH Proc Natl Acad Sci U S A. 2015 Feb 2. pii: 201420317. PMID:25646489<ref>PMID:25646489</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3j9a" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Human herpesvirus 8]]~~	+
-	~~[[Category: Dai, X]]~~	+
-	~~[[Category: Gong, D]]~~	+
-	~~[[Category: Sun, R]]~~	+
-	~~[[Category: Wu, T T]]~~	+
-	~~[[Category: Xiao, Y]]~~	+
-	~~[[Category: Zhou, H]]~~	+
-	~~[[Category: Cementing protein]]~~	+
-	~~[[Category: Viral protein]]~~	+

OCA at 19:59, 15 December 2016

OCA — Thu, 15 Dec 2016 19:59:26 GMT

←Older revision		Revision as of 19:59, 15 December 2016
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		+
	==Backbone model of the smallest capsid protein (SCP) of Kaposi's sarcoma-associated herpesvirus (KSHV)==		==Backbone model of the smallest capsid protein (SCP) of Kaposi's sarcoma-associated herpesvirus (KSHV)==
	<StructureSection load='3j9a' size='340' side='right' caption='[[3j9a]], [[Resolution\|resolution]] 6.00Å' scene=''>		<StructureSection load='3j9a' size='340' side='right' caption='[[3j9a]], [[Resolution\|resolution]] 6.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j9a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9A FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j9a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9A 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=3j9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j9a RCSB], [http://www.ebi.ac.uk/pdbsum/3j9a 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=3j9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9a OCA], [http://pdbe.org/3j9a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j9a RCSB], [http://www.ebi.ac.uk/pdbsum/3j9a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	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 3j9a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:13, 18 February 2015

OCA — Wed, 18 Feb 2015 07:13:21 GMT

←Older revision		Revision as of 07:13, 18 February 2015
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/VP26_HHV8P VP26_HHV8P]] Participates in the assembly of the infectious particles by decorating the outer surface of the capsid shell and thus forming a layer between the capsid and the tegument. Complexes composed of the major capsid protein ORF25 and VP26 assemble together in the host cytoplasm and are translocated to the nucleus, where they accumulate and participate in capsid assembly (By similarity).		[[http://www.uniprot.org/uniprot/VP26_HHV8P VP26_HHV8P]] Participates in the assembly of the infectious particles by decorating the outer surface of the capsid shell and thus forming a layer between the capsid and the tegument. Complexes composed of the major capsid protein ORF25 and VP26 assemble together in the host cytoplasm and are translocated to the nucleus, where they accumulate and participate in capsid assembly (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	With just one eighth the size of the major capsid protein (MCP), the smallest capsid protein (SCP) of human tumor herpesviruses-Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV)-is vital to capsid assembly, yet its mechanism of action is unknown. Here, by cryoEM of KSHV at 6-A resolution, we show that SCP forms a crown on each hexon and uses a kinked helix to cross-link neighboring MCP subunits. SCP-null mutation decreased viral titer by 1,000 times and impaired but did not fully abolish capsid assembly, indicating an important but nonessential role of SCP. By truncating the C-terminal half of SCP and performing cryoEM reconstruction, we demonstrate that SCP's N-terminal half is responsible for the observed structure and function whereas the C-terminal half is flexible and dispensable. Serial truncations further highlight the critical importance of the N-terminal 10 aa, and cryoEM reconstruction of the one with six residues truncated localizes the N terminus of SCP in the cryoEM density map and enables us to construct a pseudoatomic model of SCP. Fitting of this SCP model and a homology model for the MCP upper domain into the cryoEM map reveals that SCP binds MCP largely via hydrophobic interactions and the kinked helix of SCP bridges over neighboring MCPs to form noncovalent cross-links. These data support a mechanistic model that tumor herpesvirus SCP reinforces the capsid for genome packaging, thus acting as a cementing protein similar to those found in many bacteriophages.
		+
		+	CryoEM and mutagenesis reveal that the smallest capsid protein cements and stabilizes Kaposi's sarcoma-associated herpesvirus capsid.,Dai X, Gong D, Xiao Y, Wu TT, Sun R, Zhou ZH Proc Natl Acad Sci U S A. 2015 Feb 2. pii: 201420317. PMID:25646489<ref>PMID:25646489</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:53, 7 February 2015

OCA — Sat, 07 Feb 2015 15:53:00 GMT

←Older revision		Revision as of 15:53, 7 February 2015
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	==Backbone model of the smallest capsid protein (SCP) of Kaposi's sarcoma-associated herpesvirus (KSHV)==
-		+	<StructureSection load='3j9a' size='340' side='right' caption='[[3j9a]], [[Resolution\|resolution]] 6.00Å' scene=''>
-	~~The entry 3j9a is ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3j9a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_8 Human herpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9A FirstGlance]. <br>
-	~~Authors: Dai, X., Gong, D., Xiao, Y., Wu, T.-T., Sun, R., Zhou, H.~~	+	</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=3j9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j9a RCSB], [http://www.ebi.ac.uk/pdbsum/3j9a PDBsum]</span></td></tr>
-		+	</table>
-	~~Description:~~ Backbone model of the smallest capsid protein (SCP) of Kaposi's sarcoma-associated herpesvirus (KSHV)	+	== Function ==
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	[[http://www.uniprot.org/uniprot/VP26_HHV8P VP26_HHV8P]] Participates in the assembly of the infectious particles by decorating the outer surface of the capsid shell and thus forming a layer between the capsid and the tegument. Complexes composed of the major capsid protein ORF25 and VP26 assemble together in the host cytoplasm and are translocated to the nucleus, where they accumulate and participate in capsid assembly (By similarity).
-	[[~~Category~~: ~~Xiao~~, Y]]	+	__TOC__
-	[[~~Category~~: ~~Zhou, H~~]]	+	</StructureSection>
-	[[Category: ~~Gong, D~~]]	+	[[Category: Human herpesvirus 8]]
	[[Category: Dai, X]]		[[Category: Dai, X]]
-	[[Category: Wu, ~~T.-T~~]]	+	[[Category: Gong, D]]
	[[Category: Sun, R]]		[[Category: Sun, R]]
		+	[[Category: Wu, T T]]
		+	[[Category: Xiao, Y]]
		+	[[Category: Zhou, H]]
		+	[[Category: Cementing protein]]
		+	[[Category: Viral protein]]

OCA at 09:56, 31 December 2014

OCA — Wed, 31 Dec 2014 09:56:25 GMT

←Older revision		Revision as of 09:56, 31 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3j9a is ON HOLD	+	The entry 3j9a is ON HOLD until Paper Publication

	Authors: Dai, X., Gong, D., Xiao, Y., Wu, T.-T., Sun, R., Zhou, H.		Authors: Dai, X., Gong, D., Xiao, Y., Wu, T.-T., Sun, R., Zhou, H.

OCA at 12:43, 24 December 2014

OCA — Wed, 24 Dec 2014 12:43:00 GMT

←Older revision		Revision as of 12:43, 24 December 2014
Line 6:		Line 6:

	Description: Backbone model of the smallest capsid protein (SCP) of Kaposi's sarcoma-associated herpesvirus (KSHV)		Description: Backbone model of the smallest capsid protein (SCP) of Kaposi's sarcoma-associated herpesvirus (KSHV)
		+	[[Category: Unreleased Structures]]
		+	[[Category: Xiao, Y]]
		+	[[Category: Zhou, H]]
		+	[[Category: Gong, D]]
		+	[[Category: Dai, X]]
		+	[[Category: Wu, T.-T]]
		+	[[Category: Sun, R]]

OCA: Protected "3j9a" [edit=sysop:move=sysop]

OCA — Wed, 17 Dec 2014 10:43:16 GMT

Protected "3j9a" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:43, 17 December 2014

OCA: New page: '''Unreleased structure''' The entry 3j9a is ON HOLD Authors: Dai, X., Gong, D., Xiao, Y., Wu, T.-T., Sun, R., Zhou, H. Description: Backbone model of the smallest capsid protein (SCP)...

OCA — Wed, 17 Dec 2014 10:43:15 GMT

New page: '''Unreleased structure''' The entry 3j9a is ON HOLD Authors: Dai, X., Gong, D., Xiao, Y., Wu, T.-T., Sun, R., Zhou, H. Description: Backbone model of the smallest capsid protein (SCP)...

New page

'''Unreleased structure'''

The entry 3j9a is ON HOLD

Authors: Dai, X., Gong, D., Xiao, Y., Wu, T.-T., Sun, R., Zhou, H.

Description: Backbone model of the smallest capsid protein (SCP) of Kaposi's sarcoma-associated herpesvirus (KSHV)