3iys - Revision history

OCA at 10:08, 21 February 2024

OCA — Wed, 21 Feb 2024 10:08:07 GMT

←Older revision		Revision as of 10:08, 21 February 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).		[https://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting beta-hairpin observed in other polyomaviruses. We postulate that the terminal beta-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.
-
-	The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.,Shen PS, Enderlein D, Nelson CD, Carter WS, Kawano M, Xing L, Swenson RD, Olson NH, Baker TS, Cheng RH, Atwood WJ, Johne R, Belnap DM Virology. 2011 Jan 14. PMID:21239031<ref>PMID:21239031</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3iys" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]		*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>

OCA at 14:11, 24 January 2024

OCA — Wed, 24 Jan 2024 14:11:08 GMT

←Older revision		Revision as of 14:11, 24 January 2024
Line 3:		Line 3:
	<SX load='3iys' size='340' side='right' viewer='molstar' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>		<SX load='3iys' size='340' side='right' viewer='molstar' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease~~ polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aves_polyomavirus_1 Aves polyomavirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYS FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>[[~~1sie~~\|~~1sie~~]]~~</div>~~</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]] 11.3Å</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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [https://pdbe.org/3iys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [https://www.ebi.ac.uk/pdbsum/3iys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iys 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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [https://pdbe.org/3iys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [https://www.ebi.ac.uk/pdbsum/3iys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iys ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV]] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).	+	[https://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Budgerigar fledgling disease~~ polyomavirus]]	+	[[Category: Aves polyomavirus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Atwood~~, W J~~]]	+	[[Category: Atwood WJ]]
-	[[Category: Baker~~, T S~~]]	+	[[Category: Baker TS]]
-	[[Category: Belnap~~, D M~~]]	+	[[Category: Belnap DM]]
-	[[Category: Carter~~, W S~~]]	+	[[Category: Carter WS]]
-	[[Category: Cheng~~, R H~~]]	+	[[Category: Cheng RH]]
-	[[Category: Enderlein, D]]	+	[[Category: Enderlein D]]
-	[[Category: Johne, R]]	+	[[Category: Johne R]]
-	[[Category: Kawano, M]]	+	[[Category: Kawano M]]
-	[[Category: Nelson~~, C D.S~~]]	+	[[Category: Nelson CDS]]
-	[[Category: Olson~~, N H~~]]	+	[[Category: Olson NH]]
-	[[Category: Shen~~, P S~~]]	+	[[Category: Shen PS]]
-	[[Category: Swenson~~, R D~~]]	+	[[Category: Swenson RD]]
-	[[Category: Xing, L]]	+	[[Category: Xing L]]
-	~~[[Category: Apv]]~~	+
-	~~[[Category: Avian]]~~	+
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Polyomavirus]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 03:45, 21 April 2022

OCA — Thu, 21 Apr 2022 03:45:54 GMT

←Older revision		Revision as of 03:45, 21 April 2022
Line 3:		Line 3:
	<SX load='3iys' size='340' side='right' viewer='molstar' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>		<SX load='3iys' size='340' side='right' viewer='molstar' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3IYS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYS FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sie\|1sie]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1sie\|1sie]]</div></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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [~~http~~://pdbe.org/3iys PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3iys PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3iys 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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [https://pdbe.org/3iys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [https://www.ebi.ac.uk/pdbsum/3iys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iys ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV]] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).	+	[[https://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV]] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 3iys" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3iys" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:30, 10 April 2020

OCA — Fri, 10 Apr 2020 17:30:53 GMT

←Older revision		Revision as of 17:30, 10 April 2020
Line 3:		Line 3:
	<SX load='3iys' size='340' side='right' viewer='molstar' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>		<SX load='3iys' size='340' side='right' viewer='molstar' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IYS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3IYS FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sie\|1sie]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sie\|1sie]]</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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [http://pdbe.org/3iys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [http://www.ebi.ac.uk/pdbsum/3iys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iys 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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [http://pdbe.org/3iys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [http://www.ebi.ac.uk/pdbsum/3iys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iys ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 04:25, 5 March 2020

OCA — Thu, 05 Mar 2020 04:25:58 GMT

←Older revision		Revision as of 04:25, 5 March 2020
Line 1:		Line 1:

	==Homology model of avian polyomavirus asymmetric unit==		==Homology model of avian polyomavirus asymmetric unit==
-	<~~StructureSection~~ load='3iys' size='340' side='right' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>	+	<SX load='3iys' size='340' side='right' viewer='molstar' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYS FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Budgerigar fledgling disease polyomavirus]]		[[Category: Budgerigar fledgling disease polyomavirus]]
		+	[[Category: Large Structures]]
	[[Category: Atwood, W J]]		[[Category: Atwood, W J]]
	[[Category: Baker, T S]]		[[Category: Baker, T S]]

OCA at 20:12, 4 August 2016

OCA — Thu, 04 Aug 2016 20:12:34 GMT

←Older revision		Revision as of 20:12, 4 August 2016
Line 1:		Line 1:
		+
	==Homology model of avian polyomavirus asymmetric unit==		==Homology model of avian polyomavirus asymmetric unit==
	<StructureSection load='3iys' size='340' side='right' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>		<StructureSection load='3iys' size='340' side='right' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYS FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sie\|1sie]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sie\|1sie]]</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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [http://www.ebi.ac.uk/pdbsum/3iys PDBsum]</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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [http://pdbe.org/3iys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [http://www.ebi.ac.uk/pdbsum/3iys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iys ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	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 3iys" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:44, 25 December 2014

OCA — Thu, 25 Dec 2014 12:44:17 GMT

←Older revision		Revision as of 12:44, 25 December 2014
Line 6:		Line 6:
	<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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [http://www.ebi.ac.uk/pdbsum/3iys PDBsum]</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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [http://www.ebi.ac.uk/pdbsum/3iys PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV]] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 17:27, 18 December 2014

OCA — Thu, 18 Dec 2014 17:27:03 GMT

←Older revision		Revision as of 17:27, 18 December 2014
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-	~~{{STRUCTURE_3iys\| PDB=3iys \| SCENE= }}~~	+	==Homology model of avian polyomavirus asymmetric unit==
-	===Homology model of avian polyomavirus asymmetric unit===	+	<StructureSection load='3iys' size='340' side='right' caption='[[3iys]], [[Resolution\|resolution]] 11.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21239031}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3iys]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYS FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sie\|1sie]]</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=3iys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iys OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iys RCSB], [http://www.ebi.ac.uk/pdbsum/3iys PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting beta-hairpin observed in other polyomaviruses. We postulate that the terminal beta-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.

-	~~==Function==~~	+	The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.,Shen PS, Enderlein D, Nelson CD, Carter WS, Kawano M, Xing L, Swenson RD, Olson NH, Baker TS, Cheng RH, Atwood WJ, Johne R, Belnap DM Virology. 2011 Jan 14. PMID:21239031<ref>PMID:21239031</ref>
-	~~[[http://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV]] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter.~~ The ~~capsid is composed~~ of ~~72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached~~, ~~the virion is internalized by endocytosis~~ and ~~traffics to~~ the ~~endoplasmic reticulum~~. ~~Inside the endoplasmic reticulum~~, ~~the protein folding machinery isomerizes VP1 interpentamer disulfide bonds~~, ~~thereby triggering initial uncoating. Next~~, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, ~~neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus~~, ~~and participates in rearranging nucleosomes around the viral DNA (By similarity)~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3iys]] is~~ a ~~6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Budgerigar_fledgling_disease_polyomavirus Budgerigar fledgling disease polyomavirus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IYS OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021239031</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Budgerigar fledgling disease polyomavirus]]		[[Category: Budgerigar fledgling disease polyomavirus]]
-	[[Category: Atwood, W J.]]	+	[[Category: Atwood, W J]]
-	[[Category: Baker, T S.]]	+	[[Category: Baker, T S]]
-	[[Category: Belnap, D M.]]	+	[[Category: Belnap, D M]]
-	[[Category: Carter, W S.]]	+	[[Category: Carter, W S]]
-	[[Category: Cheng, R H.]]	+	[[Category: Cheng, R H]]
-	[[Category: Enderlein, D.]]	+	[[Category: Enderlein, D]]
-	[[Category: Johne, R.]]	+	[[Category: Johne, R]]
-	[[Category: Kawano, M.]]	+	[[Category: Kawano, M]]
-	[[Category: Nelson, C D.S.]]	+	[[Category: Nelson, C D.S]]
-	[[Category: Olson, N H.]]	+	[[Category: Olson, N H]]
-	[[Category: Shen, P S.]]	+	[[Category: Shen, P S]]
-	[[Category: Swenson, R D.]]	+	[[Category: Swenson, R D]]
-	[[Category: Xing, L.]]	+	[[Category: Xing, L]]
	[[Category: Apv]]		[[Category: Apv]]
	[[Category: Avian]]		[[Category: Avian]]

OCA at 09:20, 27 March 2013

OCA — Wed, 27 Mar 2013 09:20:15 GMT

←Older revision		Revision as of 09:20, 27 March 2013
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-	[[Image:3iys.png\|left\|200px]]
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-	<!--
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	{{STRUCTURE_3iys\| PDB=3iys \| SCENE= }}		{{STRUCTURE_3iys\| PDB=3iys \| SCENE= }}
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	===Homology model of avian polyomavirus asymmetric unit===		===Homology model of avian polyomavirus asymmetric unit===
		+	{{ABSTRACT_PUBMED_21239031}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/VP1_BFPYV VP1_BFPYV]] Forms an icosahedral capsid with a T=7 symmetry and a 46-48 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21239031}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov)~~, ~~where 21239031~~ is the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21239031}}~~	+

	==About this Structure==		==About this Structure==
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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21239031~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021239031</ref><references group="xtra"/><references/>
	[[Category: Budgerigar fledgling disease polyomavirus]]		[[Category: Budgerigar fledgling disease polyomavirus]]
	[[Category: Atwood, W J.]]		[[Category: Atwood, W J.]]
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	[[Category: Swenson, R D.]]		[[Category: Swenson, R D.]]
	[[Category: Xing, L.]]		[[Category: Xing, L.]]
		+	[[Category: Apv]]
		+	[[Category: Avian]]
		+	[[Category: Icosahedral virus]]
		+	[[Category: Polyomavirus]]
		+	[[Category: Virus]]

OCA at 05:42, 9 March 2011

OCA — Wed, 09 Mar 2011 05:42:10 GMT

←Older revision		Revision as of 05:42, 9 March 2011
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