5vsm - Revision history

OCA at 14:12, 13 March 2024

OCA — Wed, 13 Mar 2024 14:12:24 GMT

←Older revision		Revision as of 14:12, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='5vsm' size='340' side='right'caption='[[5vsm]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5vsm' size='340' side='right'caption='[[5vsm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vsm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VSM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VSM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vsm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VSM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VSM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=5AD:5~~-~~DEOXYADENOSINE'>5AD</scene>~~, ~~<scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>~~</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5vsl\|5vsl]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]<~~/b></td>~~<td class="sblockDat">Rsad2, Vig1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])~~</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=5vsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vsm OCA], [https://pdbe.org/5vsm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vsm RCSB], [https://www.ebi.ac.uk/pdbsum/5vsm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vsm 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=5vsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vsm OCA], [~~http~~://pdbe.org/5vsm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vsm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vsm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vsm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RSAD2_MOUSE RSAD2_MOUSE]] Interferon-inducible iron-sulfur (4FE-4S) cluster-binding antiviral protein which plays a major role in the cell antiviral state induced by type I and type II interferon. Can inhibit a wide range of viruses, including west Nile virus (WNV), dengue virus, sindbis virus, influenza A virus, sendai virus and vesicular stomatitis virus (VSV). Displays antiviral activity against influenza A virus by inhibiting the budding of the virus from the plasma membrane by disturbing the lipid rafts. This is accomplished, at least in part, through binding and inhibition of the enzyme farnesyl diphosphate synthase (FPPS), which is essential for the biosynthesis of isoprenoid-derived lipids. Promotes TLR7 and TLR9-dependent production of IFN-beta production in plasmacytoid dendritic cells (pDCs) by facilitating Lys-63'-linked ubiquitination of IRAK1. Plays a role in CD4+ T-cells activation and differentiation. Facilitates T-cell receptor (TCR)-mediated GATA3 activation and optimal T-helper 2 (Th2) cytokine production by modulating NFKB1 and JUNB activities. Can inhibit secretion of soluble proteins.<ref>PMID:17686841</ref> <ref>PMID:19047684</ref> <ref>PMID:21435586</ref> <ref>PMID:21880757</ref>	+	[https://www.uniprot.org/uniprot/RSAD2_MOUSE RSAD2_MOUSE] Interferon-inducible iron-sulfur (4FE-4S) cluster-binding antiviral protein which plays a major role in the cell antiviral state induced by type I and type II interferon. Can inhibit a wide range of viruses, including west Nile virus (WNV), dengue virus, sindbis virus, influenza A virus, sendai virus and vesicular stomatitis virus (VSV). Displays antiviral activity against influenza A virus by inhibiting the budding of the virus from the plasma membrane by disturbing the lipid rafts. This is accomplished, at least in part, through binding and inhibition of the enzyme farnesyl diphosphate synthase (FPPS), which is essential for the biosynthesis of isoprenoid-derived lipids. Promotes TLR7 and TLR9-dependent production of IFN-beta production in plasmacytoid dendritic cells (pDCs) by facilitating Lys-63'-linked ubiquitination of IRAK1. Plays a role in CD4+ T-cells activation and differentiation. Facilitates T-cell receptor (TCR)-mediated GATA3 activation and optimal T-helper 2 (Th2) cytokine production by modulating NFKB1 and JUNB activities. Can inhibit secretion of soluble proteins.<ref>PMID:17686841</ref> <ref>PMID:19047684</ref> <ref>PMID:21435586</ref> <ref>PMID:21880757</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S-adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (betaalpha)6-barrel fold with a disordered N-terminal extension (residues 45-74) and a partially ordered C-terminal extension (residues 285-362) that bridges the partial barrel to form an overall closed barrel structure. Cys84, Cys88, and Cys91 located after the first beta-strand bind a [4Fe-4S] cluster. The active site architecture of viperin with bound SAH (a SAM analog) or 5'-dAdo and l-Met (SAM cleavage products) is consistent with the canonical mechanism of 5'-deoxyadenosyl radical generation. The viperin structure, together with sequence alignments, suggests that vertebrate viperins are highly conserved and that fungi contain a viperin-like ortholog. Many bacteria and archaebacteria also express viperin-like enzymes with conserved active site residues. Structural alignments show that viperin is similar to several other radical SAM enzymes, including the molybdenum cofactor biosynthetic enzyme MoaA and the RNA methyltransferase RlmN, which methylates specific nucleotides in rRNA and tRNA. The viperin putative active site contains several conserved positively charged residues, and a portion of the active site shows structural similarity to the GTP-binding site of MoaA, suggesting that the viperin substrate may be a nucleoside triphosphate of some type.	+
-		+
-	Structural studies of viperin, an antiviral radical SAM enzyme.,Fenwick MK, Li Y, Cresswell P, Modis Y, Ealick SE Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):6806-6811. doi:, 10.1073/pnas.1705402114. Epub 2017 Jun 12. PMID:28607080<ref>PMID:28607080</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5vsm" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 15:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Cresswell, P]]	+	[[Category: Cresswell P]]
-	[[Category: Ealick~~, S E~~]]	+	[[Category: Ealick SE]]
-	[[Category: Fenwick~~, M K~~]]	+	[[Category: Fenwick MK]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	[[Category: Modis, Y]]	+	[[Category: Modis Y]]
-	~~[[Category: Antiviral protein]]~~	+
-	~~[[Category: Antiviral response]]~~	+
-	~~[[Category: Iron-sulfur cluster]]~~	+
-	~~[[Category: Radical]]~~	+
-	~~[[Category: S-adenosylmethionine~~]]	+

OCA at 16:56, 20 November 2019

OCA — Wed, 20 Nov 2019 16:56:57 GMT

←Older revision		Revision as of 16:56, 20 November 2019
Line 1:		Line 1:

	==Crystal structure of viperin with bound [4Fe-4S] cluster, 5'-deoxyadenosine, and L-methionine==		==Crystal structure of viperin with bound [4Fe-4S] cluster, 5'-deoxyadenosine, and L-methionine==
-	<StructureSection load='5vsm' size='340' side='right' caption='[[5vsm]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5vsm' size='340' side='right'caption='[[5vsm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vsm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VSM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VSM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vsm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VSM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VSM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vsl\|5vsl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vsl\|5vsl]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rsad2, Vig1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5vsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vsm OCA], [http://pdbe.org/5vsm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vsm RCSB], [http://www.ebi.ac.uk/pdbsum/5vsm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vsm 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=5vsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vsm OCA], [http://pdbe.org/5vsm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vsm RCSB], [http://www.ebi.ac.uk/pdbsum/5vsm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vsm ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Cresswell, P]]		[[Category: Cresswell, P]]
	[[Category: Ealick, S E]]		[[Category: Ealick, S E]]

OCA at 08:48, 3 August 2017

OCA — Thu, 03 Aug 2017 08:48:03 GMT

←Older revision		Revision as of 08:48, 3 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vsm is ~~ON HOLD~~	+	==Crystal structure of viperin with bound [4Fe-4S] cluster, 5'-deoxyadenosine, and L-methionine==
		+	<StructureSection load='5vsm' size='340' side='right' caption='[[5vsm]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vsm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VSM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VSM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vsl\|5vsl]]</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=5vsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vsm OCA], [http://pdbe.org/5vsm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vsm RCSB], [http://www.ebi.ac.uk/pdbsum/5vsm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vsm ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RSAD2_MOUSE RSAD2_MOUSE]] Interferon-inducible iron-sulfur (4FE-4S) cluster-binding antiviral protein which plays a major role in the cell antiviral state induced by type I and type II interferon. Can inhibit a wide range of viruses, including west Nile virus (WNV), dengue virus, sindbis virus, influenza A virus, sendai virus and vesicular stomatitis virus (VSV). Displays antiviral activity against influenza A virus by inhibiting the budding of the virus from the plasma membrane by disturbing the lipid rafts. This is accomplished, at least in part, through binding and inhibition of the enzyme farnesyl diphosphate synthase (FPPS), which is essential for the biosynthesis of isoprenoid-derived lipids. Promotes TLR7 and TLR9-dependent production of IFN-beta production in plasmacytoid dendritic cells (pDCs) by facilitating Lys-63'-linked ubiquitination of IRAK1. Plays a role in CD4+ T-cells activation and differentiation. Facilitates T-cell receptor (TCR)-mediated GATA3 activation and optimal T-helper 2 (Th2) cytokine production by modulating NFKB1 and JUNB activities. Can inhibit secretion of soluble proteins.<ref>PMID:17686841</ref> <ref>PMID:19047684</ref> <ref>PMID:21435586</ref> <ref>PMID:21880757</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Viperin is an IFN-inducible radical S-adenosylmethionine (SAM) enzyme that inhibits viral replication. We determined crystal structures of an anaerobically prepared fragment of mouse viperin (residues 45-362) complexed with S-adenosylhomocysteine (SAH) or 5'-deoxyadenosine (5'-dAdo) and l-methionine (l-Met). Viperin contains a partial (betaalpha)6-barrel fold with a disordered N-terminal extension (residues 45-74) and a partially ordered C-terminal extension (residues 285-362) that bridges the partial barrel to form an overall closed barrel structure. Cys84, Cys88, and Cys91 located after the first beta-strand bind a [4Fe-4S] cluster. The active site architecture of viperin with bound SAH (a SAM analog) or 5'-dAdo and l-Met (SAM cleavage products) is consistent with the canonical mechanism of 5'-deoxyadenosyl radical generation. The viperin structure, together with sequence alignments, suggests that vertebrate viperins are highly conserved and that fungi contain a viperin-like ortholog. Many bacteria and archaebacteria also express viperin-like enzymes with conserved active site residues. Structural alignments show that viperin is similar to several other radical SAM enzymes, including the molybdenum cofactor biosynthetic enzyme MoaA and the RNA methyltransferase RlmN, which methylates specific nucleotides in rRNA and tRNA. The viperin putative active site contains several conserved positively charged residues, and a portion of the active site shows structural similarity to the GTP-binding site of MoaA, suggesting that the viperin substrate may be a nucleoside triphosphate of some type.

-	~~Authors~~:	+	Structural studies of viperin, an antiviral radical SAM enzyme.,Fenwick MK, Li Y, Cresswell P, Modis Y, Ealick SE Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):6806-6811. doi:, 10.1073/pnas.1705402114. Epub 2017 Jun 12. PMID:28607080<ref>PMID:28607080</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vsm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cresswell, P]]
		+	[[Category: Ealick, S E]]
		+	[[Category: Fenwick, M K]]
		+	[[Category: Li, Y]]
		+	[[Category: Modis, Y]]
		+	[[Category: Antiviral protein]]
		+	[[Category: Antiviral response]]
		+	[[Category: Iron-sulfur cluster]]
		+	[[Category: Radical]]
		+	[[Category: S-adenosylmethionine]]

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

OCA — Wed, 17 May 2017 14:12:34 GMT

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

←Older revision

Revision as of 14:12, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vsm is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 May 2017 14:12:33 GMT

New page: '''Unreleased structure''' The entry 5vsm is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vsm is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]