2gef - Revision history

OCA at 10:38, 14 December 2022

OCA — Wed, 14 Dec 2022 10:38:26 GMT

←Older revision		Revision as of 10:38, 14 December 2022
Line 3:		Line 3:
	<StructureSection load='2gef' size='340' side='right'caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2gef' size='340' side='right'caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bsnv Bsnv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Blotched_snakehead_virus Blotched snakehead virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEF FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 BSNV])~~</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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [https://pdbe.org/2gef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [https://www.ebi.ac.uk/pdbsum/2gef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gef 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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [https://pdbe.org/2gef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [https://www.ebi.ac.uk/pdbsum/2gef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gef ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLS_BSNV POLS_BSNV]] 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 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 pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pre-VP2 C-terminus. It is essential for the virus viability (By similarity).	+	[https://www.uniprot.org/uniprot/POLS_BSNV POLS_BSNV] 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 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 pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pre-VP2 C-terminus. It is essential for the virus viability (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bsnv~~]]	+	[[Category: Blotched snakehead virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Delmas, B]]	+	[[Category: Delmas B]]
-	[[Category: Feldman~~, A R~~]]	+	[[Category: Feldman AR]]
-	[[Category: Lee, J]]	+	[[Category: Lee J]]
-	[[Category: Paetzel, M]]	+	[[Category: Paetzel M]]
-	~~[[Category: Birnavirus]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lysine general base]]~~	+
-	~~[[Category: Serine/lysine dyad mechamism~~]]	+

OCA at 18:59, 10 March 2021

OCA — Wed, 10 Mar 2021 18:59:04 GMT

←Older revision		Revision as of 18:59, 10 March 2021
Line 1:		Line 1:

	==Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism==		==Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism==
-	<StructureSection load='2gef' size='340' side='right' caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2gef' size='340' side='right'caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bsnv Bsnv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2GEF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bsnv Bsnv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEF FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 BSNV])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 BSNV])</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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [~~http~~://pdbe.org/2gef PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2gef PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2gef 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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [https://pdbe.org/2gef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [https://www.ebi.ac.uk/pdbsum/2gef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gef ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLS_BSNV POLS_BSNV]] 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 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 pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pre-VP2 C-terminus. It is essential for the virus viability (By similarity).	+	[[https://www.uniprot.org/uniprot/POLS_BSNV POLS_BSNV]] 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 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 pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pre-VP2 C-terminus. It is essential for the virus viability (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Bsnv]]		[[Category: Bsnv]]
		+	[[Category: Large Structures]]
	[[Category: Delmas, B]]		[[Category: Delmas, B]]
	[[Category: Feldman, A R]]		[[Category: Feldman, A R]]

OCA at 07:13, 20 June 2018

OCA — Wed, 20 Jun 2018 07:13:45 GMT

←Older revision		Revision as of 07:13, 20 June 2018
Line 1:		Line 1:
		+
	==Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism==		==Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism==
	<StructureSection load='2gef' size='340' side='right' caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2gef' size='340' side='right' caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 BSNV])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 BSNV])</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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://pdbe.org/2gef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef 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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://pdbe.org/2gef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gef ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:39, 11 September 2015

OCA — Fri, 11 Sep 2015 08:39:29 GMT

←Older revision		Revision as of 08:39, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2gef' size='340' side='right' caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2gef' size='340' side='right' caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Blotched_snakehead_virus Blotched snakehead virus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bsnv Bsnv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEF FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 ~~Blotched snakehead virus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 BSNV])</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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef 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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://pdbe.org/2gef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		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 2gef" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Blotched snakehead virus~~]]	+	[[Category: Bsnv]]
	[[Category: Delmas, B]]		[[Category: Delmas, B]]
	[[Category: Feldman, A R]]		[[Category: Feldman, A R]]

OCA at 13:59, 25 December 2014

OCA — Thu, 25 Dec 2014 13:59:34 GMT

←Older revision		Revision as of 13:59, 25 December 2014
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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef 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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLS_BSNV POLS_BSNV]] 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 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 pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pre-VP2 C-terminus. It is essential for the virus viability (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:34, 22 December 2014

OCA — Mon, 22 Dec 2014 06:34:20 GMT

←Older revision		Revision as of 06:34, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Blotched_snakehead_virus Blotched snakehead virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Blotched_snakehead_virus Blotched snakehead virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 Blotched snakehead virus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 Blotched snakehead virus])</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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef 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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Blotched snakehead virus]]		[[Category: Blotched snakehead virus]]
-	[[Category: Delmas, B.]]	+	[[Category: Delmas, B]]
-	[[Category: Feldman, A R.]]	+	[[Category: Feldman, A R]]
-	[[Category: Lee, J.]]	+	[[Category: Lee, J]]
-	[[Category: Paetzel, M.]]	+	[[Category: Paetzel, M]]
	[[Category: Birnavirus]]		[[Category: Birnavirus]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Lysine general base]]		[[Category: Lysine general base]]
	[[Category: Serine/lysine dyad mechamism]]		[[Category: Serine/lysine dyad mechamism]]

OCA at 07:04, 9 June 2014

OCA — Mon, 09 Jun 2014 07:04:40 GMT

←Older revision		Revision as of 07:04, 9 June 2014
Line 1:		Line 1:
-	[[~~Image:~~2gef.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism==
		+	<StructureSection load='2gef' size='340' side='right' caption='[[2gef]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Blotched_snakehead_virus Blotched snakehead virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birnaviridae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 Blotched snakehead virus])</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=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The blotched snakehead virus (BSNV), an aquatic birnavirus, encodes a polyprotein (NH2-pVP2-X-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease (VP4) to liberate itself and the viral proteins pVP2, X and VP3. The protein pVP2 is further processed by VP4 to give rise to the capsid protein VP2 and four structural peptides. We report here the crystal structure of a VP4 protease from BSNV, which displays a catalytic serine/lysine dyad in its active site. This is the first crystal structure of a birnavirus protease and the first crystal structure of a viral protease that utilizes a lysine general base in its catalytic mechanism. The topology of the VP4 substrate binding site is consistent with the enzymes substrate specificity and a nucleophilic attack from the si-face of the substrates scissile bond. Despite low levels of sequence identity, VP4 shows similarities in its active site to other characterized Ser/Lys proteases such as signal peptidase, LexA protease and Lon protease. Together, the structure of VP4 provides insights into the mechanism of a recently characterized clan of serine proteases that utilize a lysine general base and reveals the structure of potential targets for antiviral therapy, especially for other related and economically important viruses, such as infectious bursal disease virus in poultry and infectious pancreatic necrosis virus in aquaculture.

-	~~{{STRUCTURE_2gef\| PDB=2gef \| SCENE= }}~~	+	Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism.,Feldman AR, Lee J, Delmas B, Paetzel M J Mol Biol. 2006 May 19;358(5):1378-89. Epub 2006 Mar 6. PMID:16584747<ref>PMID:16584747</ref>

-	~~===Crystal structure of a Novel viral protease with a serine~~/~~lysine catalytic dyad mechanism===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16584747}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2gef]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Blotched_snakehead_virus Blotched snakehead virus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016584747<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Blotched snakehead virus]]		[[Category: Blotched snakehead virus]]
	[[Category: Delmas, B.]]		[[Category: Delmas, B.]]

OCA: Protected "2gef" [edit=sysop:move=sysop]

OCA — Tue, 14 Aug 2012 18:47:35 GMT

Protected "2gef" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:47, 14 August 2012

OCA at 18:47, 14 August 2012

OCA — Tue, 14 Aug 2012 18:47:33 GMT

←Older revision		Revision as of 18:47, 14 August 2012
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-	{{Seed}}
	[[Image:2gef.png\|left\|200px]]		[[Image:2gef.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2gef", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2gef\| PDB=2gef \| SCENE= }}		{{STRUCTURE_2gef\| PDB=2gef \| SCENE= }}

	===Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism===		===Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16584747}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16584747 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16584747}}		{{ABSTRACT_PUBMED_16584747}}

	==About this Structure==		==About this Structure==
-	~~2GEF is a~~ [[~~Single protein~~]] structure of sequence from [http://en.wikipedia.org/wiki/Blotched_snakehead_virus Blotched snakehead virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA].	+	[[2gef]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Blotched_snakehead_virus Blotched snakehead virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA].

	==Reference==		==Reference==
-	~~Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism., Feldman AR, Lee J, Delmas B, Paetzel M, J Mol Biol. 2006 May 19;358(5):1378-89. Epub 2006 Mar 6.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~16584747 16584747]~~	+	<ref group="xtra">PMID:016584747</ref><references group="xtra"/>
	[[Category: Blotched snakehead virus]]		[[Category: Blotched snakehead virus]]
-	[[Category: Single protein]]
	[[Category: Delmas, B.]]		[[Category: Delmas, B.]]
	[[Category: Feldman, A R.]]		[[Category: Feldman, A R.]]
Line 31:		Line 18:
	[[Category: Paetzel, M.]]		[[Category: Paetzel, M.]]
	[[Category: Birnavirus]]		[[Category: Birnavirus]]
		+	[[Category: Hydrolase]]
	[[Category: Lysine general base]]		[[Category: Lysine general base]]
	[[Category: Serine/lysine dyad mechamism]]		[[Category: Serine/lysine dyad mechamism]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 01:37:33 2008''

OCA at 22:37, 28 July 2008

OCA — Mon, 28 Jul 2008 22:37:37 GMT

←Older revision		Revision as of 22:37, 28 July 2008
Line 1:		Line 1:
-	[[Image:2gef.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2gef.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2gef\| PDB=2gef \| SCENE= }}		{{STRUCTURE_2gef\| PDB=2gef \| SCENE= }}

-	~~'''~~Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism~~'''~~	+	===Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism===


-	~~==Overview==~~	+	<!--
-	The ~~blotched snakehead virus (BSNV)~~, ~~an aquatic birnavirus~~, ~~encodes a polyprotein (NH2-pVP2-X-VP4-VP3-COOH) that is processed through~~ the ~~proteolytic activity of its own protease (VP4)~~ to ~~liberate itself and~~ the ~~viral proteins pVP2, X and VP3~~. ~~The protein pVP2 is further processed by VP4 to give rise to the capsid protein VP2 and four structural peptides~~. ~~We report here the crystal structure of a VP4 protease from BSNV~~, ~~which displays a catalytic serine/lysine dyad in its active site. This~~ is the ~~first crystal structure of a birnavirus protease and the first crystal structure of a viral protease that utilizes a lysine general base in its catalytic mechanism~~. ~~The topology of the VP4 substrate binding site is consistent with the enzymes substrate specificity and a nucleophilic attack from the si~~-face of the substrates scissile bond. Despite low levels of sequence identity, VP4 shows similarities in its active site to other characterized Ser/Lys proteases such as signal peptidase, LexA protease and Lon protease. Together, the structure of VP4 provides insights into the mechanism of a recently characterized clan of serine proteases that utilize a lysine general base and reveals the structure of potential targets for antiviral therapy, especially for other related and economically important viruses, such as infectious bursal disease virus in poultry and infectious pancreatic necrosis virus in aquaculture.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16584747}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16584747 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16584747}}

	==About this Structure==		==About this Structure==
Line 29:		Line 33:
	[[Category: Lysine general base]]		[[Category: Lysine general base]]
	[[Category: Serine/lysine dyad mechamism]]		[[Category: Serine/lysine dyad mechamism]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 05~~:00:36 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 01:37:33 2008''