5cdc - Revision history

OCA at 11:19, 10 January 2024

2024-01-10T11:19:49Z

← Older revision		Revision as of 11:19, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CDC FirstGlance]. <br>
	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [https://pdbe.org/5cdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [https://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc ProSAT]</span></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 4Å</td></tr>
			<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [https://pdbe.org/5cdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [https://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 12:00, 14 June 2023

2023-06-14T12:00:14Z

← Older revision		Revision as of 12:00, 14 June 2023
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	<StructureSection load='5cdc' size='340' side='right'caption='[[5cdc]], [[Resolution\|resolution]] 4.00Å' scene=''>		<StructureSection load='5cdc' size='340' side='right'caption='[[5cdc]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5CDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CDC FirstGlance]. <br>
	</td></tr>~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>~~		</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [https://pdbe.org/5cdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [https://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc 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=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [~~http~~://pdbe.org/5cdc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/D1FK67_9VIRU D1FK67_9VIRU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Israeli acute paralysis virus]]		[[Category: Israeli acute paralysis virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mullapudi, E]]		[[Category: Mullapudi E]]
	[[Category: Plevka, P]]		[[Category: Plevka P]]
	~~[[Category: Capsid]]~~
	~~[[Category: Honeybee virus]]~~
	~~[[Category: Pathogen]]~~
	~~[[Category: Virion]]~~
	~~[[Category: Virus~~]]

OCA at 06:24, 5 August 2020

2020-08-05T06:24:35Z

← Older revision		Revision as of 06:24, 5 August 2020
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	==Crystal Structure of Israel acute Paralysis Virus==		==Crystal Structure of Israel acute Paralysis Virus==
	<StructureSection load='5cdc' size='340' side='right' caption='[[5cdc]], [[Resolution\|resolution]] 4.00Å' scene=''>		<StructureSection load='5cdc' size='340' side='right'caption='[[5cdc]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5CDC FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></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=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [http://pdbe.org/5cdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [http://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc 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=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [http://pdbe.org/5cdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [http://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Israeli acute paralysis virus]]		[[Category: Israeli acute paralysis virus]]
			[[Category: Large Structures]]
	[[Category: Mullapudi, E]]		[[Category: Mullapudi, E]]
	[[Category: Plevka, P]]		[[Category: Plevka, P]]

OCA at 05:45, 30 May 2018

2018-05-30T05:45:48Z

← Older revision		Revision as of 05:45, 30 May 2018
Line 3:		Line 3:
	<StructureSection load='5cdc' size='340' side='right' caption='[[5cdc]], [[Resolution\|resolution]] 4.00Å' scene=''>		<StructureSection load='5cdc' size='340' side='right' caption='[[5cdc]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from ~~[http://en.wikipedia.org/wiki/Apis_mellifera Apis mellifera] and~~ [http://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CDC FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></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=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [http://pdbe.org/5cdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [http://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc 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=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [http://pdbe.org/5cdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [http://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Apis mellifera]]~~
	[[Category: Israeli acute paralysis virus]]		[[Category: Israeli acute paralysis virus]]
	[[Category: Mullapudi, E]]		[[Category: Mullapudi, E]]

OCA at 04:59, 9 September 2016

2016-09-09T04:59:36Z

← Older revision		Revision as of 04:59, 9 September 2016
Line 9:		Line 9:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	The ~~pollination services provided by the~~ western honeybee (Apis mellifera) ~~are critical for~~ the ~~agricultural production and diversity of wild flowering plants~~. However, ~~honeybees suffer~~ from ~~environmental pollution,~~ habitat loss, and pathogens, including viruses that can cause ~~fatal diseases~~. ~~Israeli acute~~ bee paralysis virus (~~IAPV~~) ~~from~~ the family ~~Dicistroviridae has been shown to cause colony collapse disorder in the United States~~. Here we present the ~~IAPV~~ virion ~~structure~~ determined to ~~a resolution~~ of 4.0 A and ~~the structure of a pentamer of capsid protein protomers at a resolution of~~ 2.7 A. ~~IAPV has~~ major capsid proteins VP1 ~~and VP3 with non~~-~~canonical jellyroll beta~~-~~barrel folds composed of only seven instead of eight beta-strands~~, ~~as is~~ the ~~rule for proteins of~~ other viruses ~~with~~ the ~~same fold.~~ The ~~maturation~~ of ~~dicistroviruses is connected to~~ the ~~cleavage~~ of ~~precursor capsid protein VP0 into subunits VP3 and VP4. We show~~ that a putative catalytic site ~~formed by residues asp-asp-phe~~ of ~~VP1 is optimally positioned to perform~~ the cleavage. ~~Furthermore, unlike many picornaviruses~~, ~~IAPV does not contain a hydrophobic pocket in~~ capsid protein ~~VP1~~ that ~~could~~ be ~~targeted by capsid-binding antiviral compounds~~. IMPORTANCE: ~~Honeybee pollination~~ is ~~required for agricultural production and~~ to sustain the biodiversity of wild flora. However, honeybee populations in Europe and North America ~~are under pressure from pathogens including~~ viruses ~~that cause colony losses. Viruses~~ from the family ~~Dicistroviridae can cause~~ honeybee ~~infections that are lethal not only to individual honeybees, but to whole colonies~~. ~~Here we present~~ the virion structure of an ~~Aparavirus Israeli acute~~ bee paralysis virus (~~IAPV~~)~~, a member of a complex of closely related viruses that are distributed worldwide~~. ~~IAPV~~ exhibits unique structural features not observed in other picorna-like viruses. ~~Capsid~~ protein ~~VP1~~ of ~~IAPV does not contain a hydrophobic pocket~~, ~~implying that capsid-binding antiviral compounds that~~ can ~~prevent~~ the ~~replication~~ of ~~vertebrate picornaviruses may~~ be ~~ineffective against honeybee virus infections~~.		The western honeybee (Apis mellifera) is the most important commercial insect pollinator. However, bees are under pressure from habitat loss, environmental stress and pathogens, including viruses that can cause lethal epidemics. Slow bee paralysis virus (SBPV) belongs to the Iflaviridae family of non-enveloped single-stranded RNA viruses. Here we present the structure of the SBPV virion determined from two crystal forms to resolutions of 3.4 A and 2.6 A. The overall structure of the virion resembles that of picornaviruses with the three major capsid proteins VP1-3 organized into a pseudo-T3 icosahedral capsid. However, the SBPV capsid protein VP3 contains a C-terminal globular domain that has not been observed in other viruses from the order Picornavirales The protruding (P)-domains form "crowns" on the virion surface around each fivefold axis in one of the crystal forms. However, the P-domains are shifted 36 A towards the threefold axis in the other crystal form. Furthermore, the P-domain contains the ser-his-asp triad within a surface patch of eight conserved residues that constitutes a putative catalytic or receptor-binding site. The movements of the domain might be required for efficient substrate cleavage or receptor binding during virus cell entry. In addition, capsid protein VP2 contains an RGD sequence that is exposed on the virion surface, indicating that integrins might be cellular receptors of SBPV. IMPORTANCE: Pollination by honeybees is needed to sustain agricultural productivity as well as the biodiversity of wild flora. However, honeybee populations in Europe and North America have been declining since the 1950s. Honeybee viruses from the Iflaviridae family are among the major causes of honeybee colony mortality. We determined the virion structure of an Iflavirus, slow bee paralysis virus (SBPV). SBPV exhibits unique structural features not observed in other picorna-like viruses. The SBPV capsid protein VP3 has a large C-terminal domain, five of which form highly prominent protruding "crowns" on the virion surface. However, the domains can change their positions depending on the conditions of the environment. The domain includes a putative catalytic or receptor binding site that might be important for SBPV cell entry.

	Virion structure of ~~Israeli acute~~ bee paralysis virus.,~~Mullapudi E~~, Pridal A, Palkova L, de Miranda JR, Plevka P J Virol. 2016 ~~Jul 6~~. pii: JVI.~~00854~~-16. PMID:~~27384649~~<ref>PMID:~~27384649~~</ref>		Virion structure of iflavirus slow bee paralysis virus at 2.6A resolution.,Kalynych S, Pridal A, Palkova L, Levdansky Y, de Miranda JR, Plevka P J Virol. 2016 Jun 8. pii: JVI.00680-16. PMID:27279610<ref>PMID:27279610</ref>

	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>

OCA at 06:48, 26 July 2016

2016-07-26T06:48:57Z

@@ Line 7: / Line 7: @@
 <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=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [http://pdbe.org/5cdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [http://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc ProSAT]</span></td></tr>
 </table>
 __TOC__
 </StructureSection>

OCA at 17:57, 13 July 2016

2016-07-13T17:57:01Z

← Older revision		Revision as of 17:57, 13 July 2016
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 5cdc is ~~ON HOLD~~		==Crystal Structure of Israel acute Paralysis Virus==
			<StructureSection load='5cdc' size='340' side='right' caption='[[5cdc]], [[Resolution\|resolution]] 4.00Å' scene=''>
	~~Authors~~: ~~Mullapudi~~, E., ~~Plevka~~, P.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5cdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Apis_mellifera Apis mellifera] and [http://en.wikipedia.org/wiki/Israeli_acute_paralysis_virus Israeli acute paralysis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CDC FirstGlance]. <br>
	~~Description~~: ~~Crystal Structure of Israel~~ acute ~~Paralysis Virus~~		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<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=5cdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cdc OCA], [http://pdbe.org/5cdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cdc RCSB], [http://www.ebi.ac.uk/pdbsum/5cdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cdc ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Apis mellifera]]
			[[Category: Israeli acute paralysis virus]]
			[[Category: Mullapudi, E]]
	[[Category: Plevka, P]]		[[Category: Plevka, P]]
	[[Category: ~~Mullapudi, E~~]]		[[Category: Capsid]]
			[[Category: Honeybee virus]]
			[[Category: Pathogen]]
			[[Category: Virion]]
			[[Category: Virus]]

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

2015-07-15T12:24:28Z

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

← Older revision	Revision as of 12:24, 15 July 2015
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5cdc is ON HOLD Authors: Mullapudi, E., Plevka, P. Description: Crystal Structure of Israel acute Paralysis Virus [[Category: Unreleased Structures...

2015-07-15T12:24:27Z

New page: '''Unreleased structure''' The entry 5cdc is ON HOLD Authors: Mullapudi, E., Plevka, P. Description: Crystal Structure of Israel acute Paralysis Virus [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 5cdc is ON HOLD

Authors: Mullapudi, E., Plevka, P.

Description: Crystal Structure of Israel acute Paralysis Virus
[[Category: Unreleased Structures]]
[[Category: Plevka, P]]
[[Category: Mullapudi, E]]