1wcd - Revision history

OCA at 09:14, 9 May 2024

2024-05-09T09:14:44Z

←Older revision		Revision as of 09:14, 9 May 2024
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	<StructureSection load='1wcd' size='340' side='right'caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1wcd' size='340' side='right'caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Avian_infectious_bursal_disease_virus Avian infectious~~ bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WCD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WCD 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;'>~~[[~~1wce~~\|~~1wce~~]]~~</div>~~</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]] 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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [https://pdbe.org/1wcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [https://www.ebi.ac.uk/pdbsum/1wcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wcd 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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [https://pdbe.org/1wcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [https://www.ebi.ac.uk/pdbsum/1wcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wcd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLS_IBDVC POLS_IBDVC]] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1 (By similarity). The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity). Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation (By similarity). Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability.	+	[https://www.uniprot.org/uniprot/POLS_IBDVC POLS_IBDVC] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1 (By similarity). The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity). Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation (By similarity). Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Avian infectious~~ bursal disease virus]]	+	[[Category: Infectious bursal disease virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bressanelli, S]]	+	[[Category: Bressanelli S]]
-	[[Category: Chevalier, C]]	+	[[Category: Chevalier C]]
-	[[Category: Coulibaly, F]]	+	[[Category: Coulibaly F]]
-	[[Category: Delmas, B]]	+	[[Category: Delmas B]]
-	[[Category: Gutsche, I]]	+	[[Category: Gutsche I]]
-	[[Category: Navaza, J]]	+	[[Category: Navaza J]]
-	[[Category: Pous, J]]	+	[[Category: Pous J]]
-	[[Category: Rey~~, F A]]~~	+	[[Category: Rey FA]]
-	~~[[Category: Birnavirus]]~~	+
-	~~[[Category: Double-stranded rna virus protein]]~~	+
-	~~[[Category: Evolution]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Membrane translocation activity]]~~	+
-	~~[[Category: Non-enveloped icosahedral viruse]]~~	+
-	~~[[Category: Transcriptase machinery]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 16:17, 27 October 2021

2021-10-27T16:17:46Z

←Older revision		Revision as of 16:17, 27 October 2021
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	<StructureSection load='1wcd' size='340' side='right'caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1wcd' size='340' side='right'caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WCD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WCD FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wce\|1wce]]</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;'>[[1wce\|1wce]]</div></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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [~~http~~://pdbe.org/1wcd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wcd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wcd 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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [https://pdbe.org/1wcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [https://www.ebi.ac.uk/pdbsum/1wcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wcd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLS_IBDVC POLS_IBDVC]] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1 (By similarity). The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity). Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation (By similarity). Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability.	+	[[https://www.uniprot.org/uniprot/POLS_IBDVC POLS_IBDVC]] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1 (By similarity). The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity). Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation (By similarity). Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 1wcd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1wcd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:05, 22 January 2020

2020-01-22T18:05:58Z

←Older revision		Revision as of 18:05, 22 January 2020
Line 1:		Line 1:

	==Crystal structure of IBDV T1 virus-like particle reveals a missing link in icosahedral viruses evolution==		==Crystal structure of IBDV T1 virus-like particle reveals a missing link in icosahedral viruses evolution==
-	<StructureSection load='1wcd' size='340' side='right' caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1wcd' size='340' side='right'caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Avian infectious bursal disease virus]]		[[Category: Avian infectious bursal disease virus]]
		+	[[Category: Large Structures]]
	[[Category: Bressanelli, S]]		[[Category: Bressanelli, S]]
	[[Category: Chevalier, C]]		[[Category: Chevalier, C]]

OCA at 16:45, 11 April 2018

2018-04-11T16:45:42Z

←Older revision		Revision as of 16:45, 11 April 2018
Line 1:		Line 1:
-	==~~CRYSTAL STRUCTURE OF~~ IBDV T1 ~~VIRUS~~-~~LIKE PARTICLE REVEALS A MISSING LINK IN ICOSAHEDRAL VIRUSES EVOLUTION~~==	+
		+	==Crystal structure of IBDV T1 virus-like particle reveals a missing link in icosahedral viruses evolution==
	<StructureSection load='1wcd' size='340' side='right' caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1wcd' size='340' side='right' caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wce\|1wce]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wce\|1wce]]</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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [http://pdbe.org/1wcd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [http://www.ebi.ac.uk/pdbsum/1wcd 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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [http://pdbe.org/1wcd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [http://www.ebi.ac.uk/pdbsum/1wcd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wcd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wc/1wcd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wc/1wcd_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 00:45, 10 February 2016

2016-02-10T00:45:05Z

←Older revision		Revision as of 00:45, 10 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wcd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:40, 11 September 2015

2015-09-11T03:40:46Z

←Older revision		Revision as of 03:40, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1wcd' size='340' side='right' caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1wcd' size='340' side='right' caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Infectious_bursal_disease_virus Infectious~~ bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wce\|1wce]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wce\|1wce]]</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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [http://www.ebi.ac.uk/pdbsum/1wcd 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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [http://pdbe.org/1wcd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [http://www.ebi.ac.uk/pdbsum/1wcd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1wcd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Infectious~~ bursal disease virus]]	+	[[Category: Avian infectious bursal disease virus]]
	[[Category: Bressanelli, S]]		[[Category: Bressanelli, S]]
	[[Category: Chevalier, C]]		[[Category: Chevalier, C]]

OCA at 10:36, 25 December 2014

2014-12-25T10:36:35Z

←Older revision		Revision as of 10:36, 25 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wce\|1wce]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wce\|1wce]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [http://www.ebi.ac.uk/pdbsum/1wcd 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=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [http://www.ebi.ac.uk/pdbsum/1wcd PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLS_IBDVC POLS_IBDVC]] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1 (By similarity). The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity). Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation (By similarity). Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing. Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
-	[[Category: Bressanelli, S.]]	+	[[Category: Bressanelli, S]]
-	[[Category: Chevalier, C.]]	+	[[Category: Chevalier, C]]
-	[[Category: Coulibaly, F.]]	+	[[Category: Coulibaly, F]]
-	[[Category: Delmas, B.]]	+	[[Category: Delmas, B]]
-	[[Category: Gutsche, I.]]	+	[[Category: Gutsche, I]]
-	[[Category: Navaza, J.]]	+	[[Category: Navaza, J]]
-	[[Category: Pous, J.]]	+	[[Category: Pous, J]]
-	[[Category: Rey, F A.]]	+	[[Category: Rey, F A]]
	[[Category: Birnavirus]]		[[Category: Birnavirus]]
	[[Category: Double-stranded rna virus protein]]		[[Category: Double-stranded rna virus protein]]

OCA at 21:41, 29 September 2014

2014-09-29T21:41:42Z

←Older revision		Revision as of 21:41, 29 September 2014
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-	[[~~Image:~~1wcd.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF IBDV T1 VIRUS-LIKE PARTICLE REVEALS A MISSING LINK IN ICOSAHEDRAL VIRUSES EVOLUTION==
		+	<StructureSection load='1wcd' size='340' side='right' caption='[[1wcd]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WCD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wce\|1wce]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wcd RCSB], [http://www.ebi.ac.uk/pdbsum/1wcd PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wc/1wcd_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Double-stranded RNA virions are transcriptionally competent icosahedral particles that must translocate across a lipid bilayer to function within the cytoplasm of the target cell. Birnaviruses are unique among dsRNA viruses as they have a single T = 13 icosahedral shell, lacking the characteristic inner capsid observed in the others. We determined the crystal structures of the T = 1 subviral particle (260 angstroms in diameter) and of the T = 13 intact virus particle (700 angstroms in diameter) of an avian birnavirus to 3 angstroms and 7 angstroms resolution, respectively. Our results show that VP2, the only component of the virus icosahedral capsid, is homologous both to the capsid protein of positive-strand RNA viruses, like the T = 3 nodaviruses, and to the T = 13 capsid protein of members of the Reoviridae family of dsRNA viruses. Together, these results provide important insights into the multiple functions of the birnavirus capsid and reveal unexpected structural relationships among icosahedral viruses.

-	~~{{STRUCTURE_1wcd\| PDB=1wcd \| SCENE= }}~~	+	The birnavirus crystal structure reveals structural relationships among icosahedral viruses.,Coulibaly F, Chevalier C, Gutsche I, Pous J, Navaza J, Bressanelli S, Delmas B, Rey FA Cell. 2005 Mar 25;120(6):761-72. PMID:15797378<ref>PMID:15797378</ref>

-	~~===CRYSTAL STRUCTURE OF IBDV T1 VIRUS-LIKE PARTICLE REVEALS A MISSING LINK IN ICOSAHEDRAL VIRUSES EVOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15797378}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1wcd]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015797378<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
	[[Category: Bressanelli, S.]]		[[Category: Bressanelli, S.]]

OCA: Protected "1wcd" [edit=sysop:move=sysop]

2013-01-05T13:06:12Z

Protected "1wcd" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:06, 5 January 2013

OCA at 13:06, 5 January 2013

2013-01-05T13:06:09Z

←Older revision		Revision as of 13:06, 5 January 2013
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-	{{Seed}}
	[[Image:1wcd.png\|left\|200px]]		[[Image:1wcd.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_1wcd\| PDB=1wcd \| SCENE= }}		{{STRUCTURE_1wcd\| PDB=1wcd \| SCENE= }}

	===CRYSTAL STRUCTURE OF IBDV T1 VIRUS-LIKE PARTICLE REVEALS A MISSING LINK IN ICOSAHEDRAL VIRUSES EVOLUTION===		===CRYSTAL STRUCTURE OF IBDV T1 VIRUS-LIKE PARTICLE REVEALS A MISSING LINK IN ICOSAHEDRAL VIRUSES EVOLUTION===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15797378}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15797378 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15797378}}		{{ABSTRACT_PUBMED_15797378}}

	==About this Structure==		==About this Structure==
-	~~1WCD~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA].	+	[[1wcd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15797378~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015797378</ref><references group="xtra"/>
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
	[[Category: Bressanelli, S.]]		[[Category: Bressanelli, S.]]
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	[[Category: Non-enveloped icosahedral viruse]]		[[Category: Non-enveloped icosahedral viruse]]
	[[Category: Transcriptase machinery]]		[[Category: Transcriptase machinery]]
-		+	[[Category: Virus]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 14:03:48 2009''~~	+