3zed: Difference between revisions

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<StructureSection load='3zed' size='340' side='right'caption='[[3zed]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3zed' size='340' side='right'caption='[[3zed]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3zed]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ipnv Ipnv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZED FirstGlance]. <br>
<table><tr><td colspan='2'>[[3zed]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Infectious_pancreatic_necrosis_virus Infectious pancreatic necrosis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZED FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.2&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=3zed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zed OCA], [https://pdbe.org/3zed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zed RCSB], [https://www.ebi.ac.uk/pdbsum/3zed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zed 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=3zed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zed OCA], [https://pdbe.org/3zed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zed RCSB], [https://www.ebi.ac.uk/pdbsum/3zed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zed ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RDRP_IPNVJ RDRP_IPNVJ]] RNA-dependent RNA polymerase which is found both free and covalently attached to the genomic RNA. May also contain guanylyl and methyl transferase activities (By similarity). [[https://www.uniprot.org/uniprot/POLS_IPNVJ POLS_IPNVJ]] 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.  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.[PROSITE-ProRule:PRU00881]  Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid composed 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 the C-terminus of pre-VP2. It destabilizes and perforates cell membranes, suggesting a role during viral entry (By similarity).  Structural peptide 2 is a small peptide derived from the C-terminus of pre-VP2. It is not essential for virus viability, but viral growth is affected when this protein is absent (By similarity).  Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for virus viability, but viral growth is affected when this protein is absent (By similarity).  
[https://www.uniprot.org/uniprot/RDRP_IPNVJ RDRP_IPNVJ] RNA-dependent RNA polymerase which is found both free and covalently attached to the genomic RNA. May also contain guanylyl and methyl transferase activities (By similarity).
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<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ipnv]]
[[Category: Infectious pancreatic necrosis virus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: RNA-directed RNA polymerase]]
[[Category: Bahar MW]]
[[Category: Bahar, M W]]
[[Category: Bamford DH]]
[[Category: Bamford, D H]]
[[Category: Graham SC]]
[[Category: Graham, S C]]
[[Category: Grimes JM]]
[[Category: Grimes, J M]]
[[Category: Pang J]]
[[Category: Pang, J]]
[[Category: Sarin LP]]
[[Category: Sarin, L P]]
[[Category: Stuart DI]]
[[Category: Stuart, D I]]
[[Category: Viral protein]]
[[Category: Virus morphogenesis]]
Retrieved from "https://proteopedia.org/3zed"