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).
<div style="background-color:#fffaf0;">
<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]]

Latest revision as of 14:00, 20 December 2023

X-ray structure of the birnavirus VP1-VP3 complexX-ray structure of the birnavirus VP1-VP3 complex

Structural highlights

3zed is a 6 chain structure with sequence from Infectious pancreatic necrosis virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).

Publication Abstract from PubMed

Infectious pancreatic necrosis virus (IPNV) - a member of the family Birnaviridae- infects young salmon, with a severe impact on the commercial sea farming industry. Of the five mature proteins encoded by the IPNV genome, the multifunctional VP3 has an essential role in morphogenesis; interacting with the capsid protein VP2, the viral double-stranded RNA (dsRNA) genome and the RNA-dependent RNA-polymerase VP1. Here we investigate one of these VP3 functions and present the crystal structure of the C-terminal 12 residues of VP3 bound to the VP1 polymerase. This interaction, visualised for the first time, reveals the precise molecular determinants used by VP3 to bind the polymerase. Competition binding studies confirm that this region of VP3 is necessary and sufficient for VP1 binding, whilst biochemical experiments show that VP3 attachment has no effect on polymerase activity. These results indicate how VP3 recruits the polymerase into birnavirus capsids during morphogenesis.

Structure of a VP1-VP3 complex suggests how birnaviruses package the VP1 polymerase.,Bahar MW, Sarin LP, Graham SC, Pang J, Bamford DH, Stuart DI, Grimes JM J Virol. 2013 Jan 2. PMID:23283942[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Bahar MW, Sarin LP, Graham SC, Pang J, Bamford DH, Stuart DI, Grimes JM. Structure of a VP1-VP3 complex suggests how birnaviruses package the VP1 polymerase. J Virol. 2013 Jan 2. PMID:23283942 doi:http://dx.doi.org/10.1128/JVI.02939-12

3zed, resolution 2.20Å

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