1sfk
From Proteopedia
(Difference between revisions)
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<StructureSection load='1sfk' size='340' side='right'caption='[[1sfk]], [[Resolution|resolution]] 3.20Å' scene=''> | <StructureSection load='1sfk' size='340' side='right'caption='[[1sfk]], [[Resolution|resolution]] 3.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1sfk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1sfk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Kunjin_virus_(STRAIN_MRM61C) Kunjin virus (STRAIN MRM61C)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SFK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 3.2Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=1sfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sfk OCA], [https://pdbe.org/1sfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sfk RCSB], [https://www.ebi.ac.uk/pdbsum/1sfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sfk 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=1sfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sfk OCA], [https://pdbe.org/1sfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sfk RCSB], [https://www.ebi.ac.uk/pdbsum/1sfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sfk ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/POLG_KUNJM POLG_KUNJM] Capsid protein C self-assembles to form an icosahedral capsid about 30 nm in diameter. The capsid encapsulates the genomic RNA (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> Non-structural protein 1 is involved in virus replication and regulation of the innate immune response (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> Non-structural protein 2A may be involved viral RNA replication and capsid assembly (Potential).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> Non-structural protein 2B is a required cofactor for the serine protease function of NS3 (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> Serine protease NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> Non-structural protein 4A induces host endoplasmic reticulum membrane rearrangements leading to the formation of virus-induced membranous vesicles hosting the dsRNA and polymerase, functioning as a replication complex. NS4A might also regulate the ATPase activity of the NS3 helicase (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> Peptide 2k functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> Non-structural protein 4B inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway (By similarity).<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway. Inhibits host JAK1 and TYK2 phosphorylation, thereby preventing activation of JAK-STAT signaling pathway.<ref>PMID:18337583</ref> <ref>PMID:20686019</ref> <ref>PMID:15650160</ref> <ref>PMID:20106931</ref> | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=1sfk 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=1sfk ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | We have determined the crystal structure of the core (C) protein from the Kunjin subtype of West Nile virus (WNV), closely related to the NY99 strain of WNV, currently a major health threat in the U.S. WNV is a member of the Flaviviridae family of enveloped RNA viruses that contains many important human pathogens. The C protein is associated with the RNA genome and forms the internal core which is surrounded by the envelope in the virion. The C protein structure contains four alpha helices and forms dimers that are organized into tetramers. The tetramers form extended filamentous ribbons resembling the stacked alpha helices seen in HEAT protein structures. | ||
| - | |||
| - | West Nile virus core protein; tetramer structure and ribbon formation.,Dokland T, Walsh M, Mackenzie JM, Khromykh AA, Ee KH, Wang S Structure. 2004 Jul;12(7):1157-63. PMID:15242592<ref>PMID:15242592</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1sfk" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Kunjm]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Dokland | + | [[Category: Dokland T]] |
| - | [[Category: Ee | + | [[Category: Ee K-H]] |
| - | [[Category: Khromykh | + | [[Category: Khromykh AA]] |
| - | [[Category: Mackenzie | + | [[Category: Mackenzie JM]] |
| - | [[Category: Walsh | + | [[Category: Walsh M]] |
| - | [[Category: Wang | + | [[Category: Wang S]] |
| - | + | ||
| - | + | ||
Current revision
Core (C) protein from West Nile Virus, subtype Kunjin
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Categories: Large Structures | Dokland T | Ee K-H | Khromykh AA | Mackenzie JM | Walsh M | Wang S
