5wtf - Revision history

OCA at 10:16, 27 March 2024

OCA — Wed, 27 Mar 2024 10:16:43 GMT

←Older revision		Revision as of 10:16, 27 March 2024
Line 3:		Line 3:
	<SX load='5wtf' size='340' side='right' viewer='molstar' caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>		<SX load='5wtf' size='340' side='right' viewer='molstar' caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hav Hav~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5WTF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepatovirus_A Hepatovirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WTF FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5wte\|5wte]]~~, [[~~5wth~~\|~~5wth~~]]</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]] 3.9Å</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=5wtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wtf OCA], [~~http~~://pdbe.org/5wtf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wtf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wtf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wtf 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=5wtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wtf OCA], [https://pdbe.org/5wtf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wtf RCSB], [https://www.ebi.ac.uk/pdbsum/5wtf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wtf ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/POLG_HAVHM POLG_HAVHM] Capsid proteins VP1, VP2, and VP3 form a closed capsid enclosing the viral positive strand RNA genome. All these proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with HAVCR1 to provide virion attachment to target cell (By similarity). Protein VP0: VP0 precursor is a component of immature procapsids. The N-terminal domain of VP0, protein VP4, is needed for the assembly of 12 pentamers into the icosahedral structure. Unlike other picornaviruses, HAV VP4 does not seem to be myristoylated and has not been detected in mature virions, supposedly owing to its small size. VP1-2A precursor is a component of immature procapsids and corresponds to an extended form of the structural protein VP1. The C-terminal domain of VP1-2A, protein 2A, acts as an assembly signal that allows pentamerization of P1-2A, which is the precursor of the structural proteins. 2A is proteolytically removed from particulate VP1-2A by a host protease and does not seem to be found in mature particles. Protein 2B and 2BC precursor affect membrane integrity and cause an increase in membrane permeability. Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor to the 3AB and 3ABC precursors. The 3AB precursor interacts with the 3CD precursor and with RNA structures found at both the 5'- and 3'-termini of the viral genome. Since the 3AB precursor contains the hydrophobic domain 3A, it probably anchors the whole viral replicase complex to intracellular membranes on which viral RNA synthesis occurs. The 3ABC precursor is targeted to the mitochondrial membrane where protease 3C activity cleaves and inhibits the host antiviral protein MAVS, thereby disrupting activation of IRF3 through the IFIH1/MDA5 pathway. In vivo, the protease activity of 3ABC precursor is more efficient in cleaving the 2BC precursor than that of protein 3C. The 3ABC precursor may therefore play a role in the proteolytic processing of the polyprotein. Protein 3B is covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. It acts as a genome-linked replication primer. Protease 3C: cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease. Also cleaves host proteins such as PCBP2. RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals.
-	~~Hepatitis A virus~~ (~~HAV~~) ~~infects approximately 1.4 million people annually~~ and, ~~although there is~~ a ~~vaccine~~, ~~there~~ are ~~no licensed therapeutic drugs~~. ~~HAV is unusually stable~~ (~~making disinfection problematic~~) ~~and little~~ is ~~known~~ of ~~how it enters cells and releases its RNA~~. ~~Here we report a potent HAV~~-~~specific monoclonal antibody~~, ~~R10~~, ~~which neutralizes~~ HAV ~~infection by blocking attachment~~ to the ~~host cell~~. ~~High~~-~~resolution cryo~~-~~EM structures~~ of ~~HAV full~~ and ~~empty~~ particles and ~~of the complex of HAV~~ with ~~R10 Fab reveal the atomic details~~ of ~~antibody~~ binding and ~~point~~ to ~~a receptor recognition site at~~ the ~~pentamer interface~~. ~~These results, together~~ with ~~our observation that~~ the ~~R10 Fab destabilizes~~ the ~~capsid~~, ~~suggest~~ the ~~use of a receptor mimic mechanism~~ to ~~neutralize virus infection~~, ~~providing new opportunities for therapeutic intervention~~.	+
-		+
-	~~Potent neutralization~~ of ~~hepatitis A virus reveals~~ a ~~receptor mimic mechanism and~~ the ~~receptor recognition site~~.~~,Wang X, Zhu L, Dang M, Hu Z, Gao Q, Yuan S, Sun Y, Zhang B, Ren J, Kotecha A, Walter TS, Wang J, Fry EE, Stuart DI, Rao Z Proc Natl Acad Sci U S A~~. ~~2017 Jan 10~~. ~~pii~~: ~~201616502~~. ~~doi:~~, 10.~~1073/pnas.1616502114. PMID:28074040<ref>PMID:28074040</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of~~ the U.S. ~~National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe~~-~~citations 5wtf" style="background~~-~~color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Hav~~]]	+	[[Category: Hepatovirus A]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dang, M]]	+	[[Category: Dang M]]
-	[[Category: Fry~~, E E~~]]	+	[[Category: Fry EE]]
-	[[Category: Gao, Q]]	+	[[Category: Gao Q]]
-	[[Category: Hu, Z]]	+	[[Category: Hu Z]]
-	[[Category: Rao, Z]]	+	[[Category: Rao Z]]
-	[[Category: Ren, J]]	+	[[Category: Ren J]]
-	[[Category: Stuart~~, D I~~]]	+	[[Category: Stuart DI]]
-	[[Category: Sun, Y]]	+	[[Category: Sun Y]]
-	[[Category: Walter~~, T S~~]]	+	[[Category: Walter TS]]
-	[[Category: Wang, J]]	+	[[Category: Wang J]]
-	[[Category: Wang, X]]	+	[[Category: Wang X]]
-	[[Category: Yuan, S]]	+	[[Category: Yuan S]]
-	[[Category: Zhang, B]]	+	[[Category: Zhang B]]
-	[[Category: Zhu, L]]	+	[[Category: Zhu L]]
-	~~[[Category: Neutralizing mechanism]]~~	+
-	~~[[Category: Receptor recognition]]~~	+
-	~~[[Category: Viral entry]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 22:29, 10 April 2020

OCA — Fri, 10 Apr 2020 22:29:05 GMT

←Older revision		Revision as of 22:29, 10 April 2020
Line 3:		Line 3:
	<SX load='5wtf' size='340' side='right' viewer='molstar' caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>		<SX load='5wtf' size='340' side='right' viewer='molstar' caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Hav Hav]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WTF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Hav Hav]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WTF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wte\|5wte]], [[5wth\|5wth]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wte\|5wte]], [[5wth\|5wth]]</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=5wtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wtf OCA], [http://pdbe.org/5wtf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wtf RCSB], [http://www.ebi.ac.uk/pdbsum/5wtf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wtf ProSAT]</span></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=5wtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wtf OCA], [http://pdbe.org/5wtf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wtf RCSB], [http://www.ebi.ac.uk/pdbsum/5wtf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wtf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:00, 6 March 2020

OCA — Fri, 06 Mar 2020 20:00:54 GMT

←Older revision		Revision as of 20:00, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure for Hepatitis A virus empty particle==		==Cryo-EM structure for Hepatitis A virus empty particle==
-	<~~StructureSection~~ load='5wtf' size='340' side='right'caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>	+	<SX load='5wtf' size='340' side='right' viewer='molstar' caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Hav Hav]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WTF FirstGlance]. <br>		<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Hav Hav]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WTF FirstGlance]. <br>
Line 19:		Line 19:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Hav]]		[[Category: Hav]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:26, 6 November 2019

OCA — Wed, 06 Nov 2019 07:26:20 GMT

←Older revision		Revision as of 07:26, 6 November 2019
Line 1:		Line 1:

	==Cryo-EM structure for Hepatitis A virus empty particle==		==Cryo-EM structure for Hepatitis A virus empty particle==
-	<StructureSection load='5wtf' size='340' side='right' caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>	+	<StructureSection load='5wtf' size='340' side='right'caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WTF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Hav Hav]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WTF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wte\|5wte]], [[5wth\|5wth]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wte\|5wte]], [[5wth\|5wth]]</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=5wtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wtf OCA], [http://pdbe.org/5wtf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wtf RCSB], [http://www.ebi.ac.uk/pdbsum/5wtf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wtf 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=5wtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wtf OCA], [http://pdbe.org/5wtf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wtf RCSB], [http://www.ebi.ac.uk/pdbsum/5wtf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wtf ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hav]]
		+	[[Category: Large Structures]]
	[[Category: Dang, M]]		[[Category: Dang, M]]
	[[Category: Fry, E E]]		[[Category: Fry, E E]]
Line 34:		Line 36:
	[[Category: Zhang, B]]		[[Category: Zhang, B]]
	[[Category: Zhu, L]]		[[Category: Zhu, L]]
-	[[Category: Hav]]
	[[Category: Neutralizing mechanism]]		[[Category: Neutralizing mechanism]]
	[[Category: Receptor recognition]]		[[Category: Receptor recognition]]
	[[Category: Viral entry]]		[[Category: Viral entry]]
	[[Category: Virus]]		[[Category: Virus]]

OCA at 23:29, 25 January 2017

OCA — Wed, 25 Jan 2017 23:29:42 GMT

←Older revision		Revision as of 23:29, 25 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wtf is ~~ON HOLD~~	+	==Cryo-EM structure for Hepatitis A virus empty particle==
		+	<StructureSection load='5wtf' size='340' side='right' caption='[[5wtf]], [[Resolution\|resolution]] 3.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wtf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WTF FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wte\|5wte]], [[5wth\|5wth]]</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=5wtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wtf OCA], [http://pdbe.org/5wtf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wtf RCSB], [http://www.ebi.ac.uk/pdbsum/5wtf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wtf ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hepatitis A virus (HAV) infects approximately 1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and little is known of how it enters cells and releases its RNA. Here we report a potent HAV-specific monoclonal antibody, R10, which neutralizes HAV infection by blocking attachment to the host cell. High-resolution cryo-EM structures of HAV full and empty particles and of the complex of HAV with R10 Fab reveal the atomic details of antibody binding and point to a receptor recognition site at the pentamer interface. These results, together with our observation that the R10 Fab destabilizes the capsid, suggest the use of a receptor mimic mechanism to neutralize virus infection, providing new opportunities for therapeutic intervention.

-	~~Authors~~:	+	Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site.,Wang X, Zhu L, Dang M, Hu Z, Gao Q, Yuan S, Sun Y, Zhang B, Ren J, Kotecha A, Walter TS, Wang J, Fry EE, Stuart DI, Rao Z Proc Natl Acad Sci U S A. 2017 Jan 10. pii: 201616502. doi:, 10.1073/pnas.1616502114. PMID:28074040<ref>PMID:28074040</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5wtf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dang, M]]
		+	[[Category: Fry, E E]]
		+	[[Category: Gao, Q]]
		+	[[Category: Hu, Z]]
		+	[[Category: Rao, Z]]
		+	[[Category: Ren, J]]
		+	[[Category: Stuart, D I]]
		+	[[Category: Sun, Y]]
		+	[[Category: Walter, T S]]
		+	[[Category: Wang, J]]
		+	[[Category: Wang, X]]
		+	[[Category: Yuan, S]]
		+	[[Category: Zhang, B]]
		+	[[Category: Zhu, L]]
		+	[[Category: Hav]]
		+	[[Category: Neutralizing mechanism]]
		+	[[Category: Receptor recognition]]
		+	[[Category: Viral entry]]
		+	[[Category: Virus]]

OCA: Protected "5wtf" [edit=sysop:move=sysop]

OCA — Thu, 22 Dec 2016 20:41:23 GMT

Protected "5wtf" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:41, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5wtf is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 22 Dec 2016 20:41:22 GMT

New page: '''Unreleased structure''' The entry 5wtf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5wtf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]