5ipi - Revision history

OCA at 12:35, 6 March 2024

2024-03-06T12:35:00Z

←Older revision		Revision as of 12:35, 6 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>		[https://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Adeno-associated viruses (AAV) are promising therapeutic gene delivery vectors and better understanding of their capsid assembly and genome packaging mechanism is needed for improved vector production. Empty AAV capsids assemble in the nucleus prior to genome packaging by virally encoded Rep proteins. To elucidate the capsid determinants of this process, structural differences between wild-type (wt) AAV2 and a packaging deficient variant, AAV2-R432A, were examined using cryo-electron microscopy and three-dimensional image reconstruction both at approximately 5.0 A (medium) and also 3.8 and 3.7 A (high) resolution, respectively. The high resolution structures showed that removal of the arginine side-chain in AAV2-R432A eliminated hydrogen bonding interactions resulting in altered intramolecular and intermolecular interactions propagated from under the 3-fold axis towards the 5-fold channel. Consistent with these observations, differential scanning calorimetry showed an approximately 10 degrees C decrease in thermal stability for AAV2-R432A compared to wt-AAV2. Additionally, the medium resolution structures revealed differences in the juxtaposition of the less ordered, N-terminal region of their capsid proteins, VP1/2/3. A structural rearrangement in AAV2-R432A repositioned the betaA strand region under the icosahedral 2-fold axis rather than anti-parallel to the betaB strand, eliminating many intramolecular interactions. Thus, a single amino acid substitution can significantly alter the AAV capsid integrity to the extent of reducing its stability and possibly rendering it unable to tolerate the stress of genome packaging. Furthermore, the data show that the 2-, 3-, and 5-fold regions of the capsid contributed to producing the packaging defect and highlight a tight connection between the entire capsid in maintaining packaging efficiency. IMPORTANCE: The mechanism of AAV genome packaging is still poorly understood, particularly with respect to the capsid determinants of the required capsid-Rep interaction. Understanding this mechanism may aid in the improvement of AAV packaging efficiency, which is currently approximately 1:10 (10%) genome packaged to empty capsid in vector preparations. This report identifies regions of the AAV capsid that play roles in genome packaging and that may be important for Rep recognition. It also demonstrates the need to maintain capsid stability for the success of this process. This information is important for efforts to improve AAV genome packaging and will also inform the engineering of AAV capsid variants for improved tropism, specific tissue targeting, and host antibody escape by defining amino acids that cannot be altered without detriment to infectious vector production.
-
-	Cryo-electron microscopy reconstruction and stability studies of Wild-Type and R432A Variant of AAV2 Reveals Capsid Structural Stability is a Major Factor in Genome Packaging.,Drouin LM, Lins B, Janssen M, Bennett A, Chipman P, McKenna R, Chen W, Muzyczka N, Cardone G, Baker TS, Agbandje-McKenna M J Virol. 2016 Jul 20. pii: JVI.00575-16. PMID:27440903<ref>PMID:27440903</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5ipi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:05, 30 August 2023

2023-08-30T14:05:05Z

←Older revision		Revision as of 14:05, 30 August 2023
Line 3:		Line 3:
	<SX load='5ipi' size='340' side='right' viewer='molstar' caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='5ipi' size='340' side='right' viewer='molstar' caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aav~~-~~2 Aav~~-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IPI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure with sequence from [https://en.wikipedia.org/wiki/Adeno-associated_virus_2 Adeno-associated virus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IPI FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5ipk\|5ipk]]</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]] 3.8Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">VP1 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10804 AAV-2])~~</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=5ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipi OCA], [https://pdbe.org/5ipi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ipi RCSB], [https://www.ebi.ac.uk/pdbsum/5ipi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipi 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=5ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipi OCA], [~~http~~://pdbe.org/5ipi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ipi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ipi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipi ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S]] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>	+	[https://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5ipi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ipi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Aav~~-2]]	+	[[Category: Adeno-associated virus 2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Agbandje-McKenna, M]]	+	[[Category: Agbandje-McKenna M]]
-	[[Category: Baker~~, T S~~]]	+	[[Category: Baker TS]]
-	[[Category: Bennet, A]]	+	[[Category: Bennet A]]
-	[[Category: Cardone, G]]	+	[[Category: Cardone G]]
-	[[Category: Chen, W]]	+	[[Category: Chen W]]
-	[[Category: Chipman, P]]	+	[[Category: Chipman P]]
-	[[Category: Drouin~~, L M~~]]	+	[[Category: Drouin LM]]
-	[[Category: Janssen~~, M E~~]]	+	[[Category: Janssen ME]]
-	[[Category: Lins, B]]	+	[[Category: Lins B]]
-	[[Category: McKenna, R]]	+	[[Category: McKenna R]]
-	[[Category: Muzyczka, N]]	+	[[Category: Muzyczka N]]
-	~~[[Category: Adeno-associated virus]]~~	+
-	~~[[Category: Dependoparvovirus]]~~	+
-	~~[[Category: Gene therapy]]~~	+
-	~~[[Category: Icosahedral]]~~	+
-	~~[[Category: Virus like particle~~]]	+

OCA at 20:15, 10 April 2020

2020-04-10T20:15:06Z

←Older revision		Revision as of 20:15, 10 April 2020
Line 3:		Line 3:
	<SX load='5ipi' size='340' side='right' viewer='molstar' caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='5ipi' size='340' side='right' viewer='molstar' caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Aav-2 Aav-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IPI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Aav-2 Aav-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IPI FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ipk\|5ipk]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ipk\|5ipk]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 AAV-2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 AAV-2])</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=5ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipi OCA], [http://pdbe.org/5ipi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipi RCSB], [http://www.ebi.ac.uk/pdbsum/5ipi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipi 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=5ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipi OCA], [http://pdbe.org/5ipi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipi RCSB], [http://www.ebi.ac.uk/pdbsum/5ipi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 18:34, 6 March 2020

2020-03-06T18:34:12Z

←Older revision		Revision as of 18:34, 6 March 2020
Line 1:		Line 1:

	==Structure of Adeno-associated virus type 2 VLP==		==Structure of Adeno-associated virus type 2 VLP==
-	<~~StructureSection~~ load='5ipi' size='340' side='right'caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<SX load='5ipi' size='340' side='right' viewer='molstar' caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Aav-2 Aav-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Aav-2 Aav-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPI FirstGlance]. <br>
Line 22:		Line 22:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Aav-2]]		[[Category: Aav-2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 09:08, 4 December 2019

2019-12-04T09:08:32Z

←Older revision		Revision as of 09:08, 4 December 2019
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Structure of Adeno-associated virus type 2 VLP==		==Structure of Adeno-associated virus type 2 VLP==
-	<StructureSection load='5ipi' size='340' side='right' caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<StructureSection load='5ipi' size='340' side='right'caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Aav-2 Aav-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPI FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ipk\|5ipk]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ipk\|5ipk]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 AAV-2])</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=5ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipi OCA], [http://pdbe.org/5ipi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipi RCSB], [http://www.ebi.ac.uk/pdbsum/5ipi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipi 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=5ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipi OCA], [http://pdbe.org/5ipi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipi RCSB], [http://www.ebi.ac.uk/pdbsum/5ipi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipi ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S]] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>		[[http://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S]] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aav-2]]
		+	[[Category: Large Structures]]
	[[Category: Agbandje-McKenna, M]]		[[Category: Agbandje-McKenna, M]]
	[[Category: Baker, T S]]		[[Category: Baker, T S]]

OCA at 20:33, 3 August 2016

2016-08-03T20:33:09Z

←Older revision		Revision as of 20:33, 3 August 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S]] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>		[[http://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S]] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Adeno-associated viruses (AAV) are promising therapeutic gene delivery vectors and better understanding of their capsid assembly and genome packaging mechanism is needed for improved vector production. Empty AAV capsids assemble in the nucleus prior to genome packaging by virally encoded Rep proteins. To elucidate the capsid determinants of this process, structural differences between wild-type (wt) AAV2 and a packaging deficient variant, AAV2-R432A, were examined using cryo-electron microscopy and three-dimensional image reconstruction both at approximately 5.0 A (medium) and also 3.8 and 3.7 A (high) resolution, respectively. The high resolution structures showed that removal of the arginine side-chain in AAV2-R432A eliminated hydrogen bonding interactions resulting in altered intramolecular and intermolecular interactions propagated from under the 3-fold axis towards the 5-fold channel. Consistent with these observations, differential scanning calorimetry showed an approximately 10 degrees C decrease in thermal stability for AAV2-R432A compared to wt-AAV2. Additionally, the medium resolution structures revealed differences in the juxtaposition of the less ordered, N-terminal region of their capsid proteins, VP1/2/3. A structural rearrangement in AAV2-R432A repositioned the betaA strand region under the icosahedral 2-fold axis rather than anti-parallel to the betaB strand, eliminating many intramolecular interactions. Thus, a single amino acid substitution can significantly alter the AAV capsid integrity to the extent of reducing its stability and possibly rendering it unable to tolerate the stress of genome packaging. Furthermore, the data show that the 2-, 3-, and 5-fold regions of the capsid contributed to producing the packaging defect and highlight a tight connection between the entire capsid in maintaining packaging efficiency. IMPORTANCE: The mechanism of AAV genome packaging is still poorly understood, particularly with respect to the capsid determinants of the required capsid-Rep interaction. Understanding this mechanism may aid in the improvement of AAV packaging efficiency, which is currently approximately 1:10 (10%) genome packaged to empty capsid in vector preparations. This report identifies regions of the AAV capsid that play roles in genome packaging and that may be important for Rep recognition. It also demonstrates the need to maintain capsid stability for the success of this process. This information is important for efforts to improve AAV genome packaging and will also inform the engineering of AAV capsid variants for improved tropism, specific tissue targeting, and host antibody escape by defining amino acids that cannot be altered without detriment to infectious vector production.
		+
		+	Cryo-electron microscopy reconstruction and stability studies of Wild-Type and R432A Variant of AAV2 Reveals Capsid Structural Stability is a Major Factor in Genome Packaging.,Drouin LM, Lins B, Janssen M, Bennett A, Chipman P, McKenna R, Chen W, Muzyczka N, Cardone G, Baker TS, Agbandje-McKenna M J Virol. 2016 Jul 20. pii: JVI.00575-16. PMID:27440903<ref>PMID:27440903</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ipi" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:39, 26 July 2016

2016-07-26T15:39:55Z

←Older revision		Revision as of 15:39, 26 July 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	{{Large structure}}
-		+	==Structure of Adeno-associated virus type 2 VLP==
-	The entry ~~5ipi is ON HOLD~~ ~~until Paper Publication~~	+	<StructureSection load='5ipi' size='340' side='right' caption='[[5ipi]], [[Resolution\|resolution]] 3.80Å' scene=''>
-		+	== Structural highlights ==
-	~~Authors~~:	+	<table><tr><td colspan='2'>[[5ipi]] is a 60 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPI FirstGlance]. <br>
-		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ipk\|5ipk]]</td></tr>
-	~~Description~~:	+	<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=5ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipi OCA], [http://pdbe.org/5ipi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipi RCSB], [http://www.ebi.ac.uk/pdbsum/5ipi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipi ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	{{Large structure}}
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAPSD_AAV2S CAPSD_AAV2S]] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus.<ref>PMID:10684294</ref> <ref>PMID:11961250</ref> <ref>PMID:16940508</ref> <ref>PMID:9445046</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Agbandje-McKenna, M]]
		+	[[Category: Baker, T S]]
		+	[[Category: Bennet, A]]
		+	[[Category: Cardone, G]]
		+	[[Category: Chen, W]]
		+	[[Category: Chipman, P]]
		+	[[Category: Drouin, L M]]
		+	[[Category: Janssen, M E]]
		+	[[Category: Lins, B]]
		+	[[Category: McKenna, R]]
		+	[[Category: Muzyczka, N]]
		+	[[Category: Adeno-associated virus]]
		+	[[Category: Dependoparvovirus]]
		+	[[Category: Gene therapy]]
		+	[[Category: Icosahedral]]
		+	[[Category: Virus like particle]]

OCA at 07:38, 14 July 2016

2016-07-14T07:38:29Z

←Older revision		Revision as of 07:38, 14 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ipi is ON HOLD	+	The entry 5ipi is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 14:37, 15 May 2016

2016-05-15T14:37:29Z

←Older revision		Revision as of 14:37, 15 May 2016
Line 3:		Line 3:
	The entry 5ipi is ON HOLD		The entry 5ipi is ON HOLD

-	Authors: ~~Drouin, L.M., Lins, B., Janssen, M.E., Bennet, A., Chipman, P., McKenna, R., Chen, W., Muzyczka, N., Cardone, G., Baker, T.S., Agbandje-McKenna, M.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Chipman, P]]
-	[[Category: Cardone, G]]
-	[[Category: Chen, W]]
-	[[Category: Drouin, L.M]]
-	[[Category: Agbandje-Mckenna, M]]
-	[[Category: Baker, T.S]]
-	[[Category: Bennet, A]]
-	[[Category: Mckenna, R]]
-	[[Category: Janssen, M.E]]
-	[[Category: Muzyczka, N]]
-	[[Category: Lins, B]]

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

2016-05-11T00:45:45Z

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

←Older revision

Revision as of 00:45, 11 May 2016