1s49: Difference between revisions

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 <StructureSection load='1s49' size='340' side='right'caption='[[1s49]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1s49]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bvdv Bvdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S49 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1S49 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1s49]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovine_viral_diarrhea_virus_1 Bovine viral diarrhea virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S49 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s48|1s48]], [[1s4f|1s4f]]</div></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=1s49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s49 OCA], [https://pdbe.org/1s49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s49 RCSB], [https://www.ebi.ac.uk/pdbsum/1s49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s49 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NS5B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11099 BVDV])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1s49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s49 OCA], [http://pdbe.org/1s49 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s49 RCSB], [http://www.ebi.ac.uk/pdbsum/1s49 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s49 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/POLG_BVDVN POLG_BVDVN]] Initial binding to target cell probably involves interaction of E(rns) with glycosaminoglycans. E1 and/or E2 are responsible of cell attachment with CD46 and subsequent fusion after internalization of the virion by endocytosis (Probable).<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   P7 forms a leader sequence to properly orient NS2 in the membrane (By similarity).<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   Uncleaved NS2-3 is required for production of infectious virus.<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase.<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   NS4A is a cofactor for the NS3 protease activity (By similarity).<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>
+[https://www.uniprot.org/uniprot/POLG_BVDVN POLG_BVDVN] Initial binding to target cell probably involves interaction of E(rns) with glycosaminoglycans. E1 and/or E2 are responsible of cell attachment with CD46 and subsequent fusion after internalization of the virion by endocytosis (Probable).<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   P7 forms a leader sequence to properly orient NS2 in the membrane (By similarity).<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   Uncleaved NS2-3 is required for production of infectious virus.<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase.<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   NS4A is a cofactor for the NS3 protease activity (By similarity).<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>   RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.<ref>PMID:14963137</ref> <ref>PMID:16051874</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 22: / Line 20: @@
 </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=1s49 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The bovine viral diarrhea virus (BVDV) RNA-dependent RNA polymerase can initiate RNA replication by a de novo mechanism without a primer. The structure of BVDV polymerase, determined to 2.9-A resolution, contains a unique N-terminal domain, in addition to the fingers, palm, and thumb domains common to other polymerases. The structure of BVDV polymerase complexed with GTP, which is required for de novo (primer-independent) initiation, shows that GTP binds adjacent to the initiation NTP, suggesting that the GTP mimics a vestigial RNA product. Comparison of five monomers in two different crystal forms showed conformational changes in the fingertip region and in the thumb domain that may help to translocate the RNA template and product strands during elongation. The putative binding sites of previously reported BVDV inhibitors are also discussed.
-The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation.,Choi KH, Groarke JM, Young DC, Kuhn RJ, Smith JL, Pevear DC, Rossmann MG Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4425-30. Epub 2004 Mar 19. PMID:15070734<ref>PMID:15070734</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1s49" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 38: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Bvdv]]
+[[Category: Bovine viral diarrhea virus 1]]
 [[Category: Large Structures]]
-[[Category: Choi, K H]]
+[[Category: Choi KH]]
-[[Category: Groarke, J M]]
+[[Category: Groarke JM]]
-[[Category: Kuhn, R J]]
+[[Category: Kuhn RJ]]
-[[Category: Pevear, D C]]
+[[Category: Pevear DC]]
-[[Category: Rossmann, M G]]
+[[Category: Rossmann MG]]
-[[Category: Smith, J L]]
+[[Category: Smith JL]]
-[[Category: Young, D C]]
+[[Category: Young DC]]
-[[Category: Bovine viral diarrhea virus]]
-[[Category: De novo initiation]]
-[[Category: Gtp binding]]
-[[Category: Polymerase]]
-[[Category: Primer independent initiation]]
-[[Category: Replication]]
-[[Category: Rna binding protein]]
-[[Category: Rna synthesis]]