P05844 (POLS_IPNVJ) Reviewed, UniProtKB/Swiss-Prot
Last modified May 1, 2013. Version 74. History...
Names and origin
|Protein names||Recommended name:|
|Organism||Infectious pancreatic necrosis virus (strain Jasper) (IPNV) [Reference proteome]|
|Taxonomic identifier||11003 [NCBI]|
|Taxonomic lineage||Viruses › dsRNA viruses › Birnaviridae › Aquabirnavirus ›|
|Virus host||Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) [TaxID: 8022]|
Salmo [TaxID: 8028]
|Sequence length||972 AA.|
|Sequence processing||The displayed sequence is further processed into a mature form.|
|Protein existence||Evidence at protein level|
General annotation (Comments)
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 By similarity.
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.
Capsid protein VP2 is a homotrimer. A central divalent metal (possibly cobalt) stabilizes the VP2 trimer. Capsid protein VP3 is a homodimer. Capsid protein VP3 interacts (via C-terminus) with VP1 in the cytoplasm. Capsid protein VP3 interacts with VP2 By similarity. Ref.3
Specific enzymatic cleavages yield mature proteins. Capsid assembly seems to be regulated by polyprotein processing. The protease VP4 cleaves itself off the polyprotein, thus releasing pre-VP2 and VP3 within the infected cell. During capsid assembly, the C-terminus of pre-VP2 is further processed by VP4, giving rise to VP2, the external capsid protein and three small peptides that all stay closely associated with the capsid.
Contains 1 peptidase S50 domain.
|Cellular component||Host cytoplasm|
|Molecular function||Capsid protein|
T=13 icosahedral capsid protein
|Gene Ontology (GO)|
Inferred from electronic annotation. Source: UniProtKB-KW
|Cellular_component||T=13 icosahedral viral capsid|
Inferred from electronic annotation. Source: UniProtKB-KWhost cell cytoplasm
Inferred from electronic annotation. Source: UniProtKB-SubCell
|Molecular_function||metal ion binding|
Inferred from electronic annotation. Source: UniProtKB-KWserine-type peptidase activity
Inferred from electronic annotation. Source: UniProtKB-KWstructural molecule activity
Inferred from electronic annotation. Source: InterPro
|Complete GO annotation...|
Sequence annotation (Features)
|Feature key||Position(s)||Length||Description||Graphical view||Feature identifier|
|Chain||1 – 972||972||Structural polyprotein||PRO_0000391632|
|Chain||1 – 508||508||Precursor of VP2||PRO_0000391633|
|Chain||1 – 442||442||Capsid protein VP2||PRO_0000036780|
|Peptide||443 – 486||44||Structural peptide 1 By similarity||PRO_0000227859|
|Peptide||487 – 495||9||Structural peptide 2 By similarity||PRO_0000227860|
|Peptide||496 – 508||13||Structural peptide 3 By similarity||PRO_0000227861|
|Chain||509 – 734||226||Protease VP4||PRO_0000036781|
|Chain||735 – 972||238||Capsid protein VP3||PRO_0000036782|
|Domain||509 – 734||226||Peptidase S50|
|Active site||633||1||Nucleophile By similarity|
|Active site||674||1||By similarity|
|Metal binding||26||1||Divalent metal cation; shared with trimeric partners|
|Site||442 – 443||2||Cleavage; by protease VP4 By similarity|
|Site||486 – 487||2||Cleavage; by protease VP4 By similarity|
|Site||495 – 496||2||Cleavage; by protease VP4 By similarity|
|Site||508 – 509||2||Cleavage; by protease VP4 By similarity|
|Site||734 – 735||2||Cleavage; by protease VP4 By similarity|
Helix Strand Turn
|Helix||968 – 970||3|
|||"The nucleotide sequence of infectious pancreatic necrosis virus (IPNV) dsRNA segment A reveals one large ORF encoding a precursor polyprotein."|
Duncan R., Dobos P.
Nucleic Acids Res. 14:5934-5934(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
|||"Synthesis of the infectious pancreatic necrosis virus polyprotein, detection of a virus-encoded protease, and fine structure mapping of genome segment A coding regions."|
Duncan R., Nagy E., Krell P.J., Dobos P.
J. Virol. 61:3655-3664(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 433-972, SEQUENCE REVISION TO 566 AND 708.
|||"Crystal structure of an aquabirnavirus particle: insights into antigenic diversity and virulence determinism."|
Coulibaly F., Chevalier C., Delmas B., Rey F.A.
J. Virol. 84:1792-1799(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, STRUCTURE BY ELECTRON MICROSCOPY (3.4 ANGSTROMS) OF SUBVIRAL PARTICLES.
|+||Additional computationally mapped references.|
|M18049 Genomic RNA. Translation: AAA89179.1.|
|PIR||GNXSIV. A23599. |
|RefSeq||NP_047196.1. NC_001915.1. |
3D structure databases
|SMR||P05844. Positions 514-716. |
Protocols and materials databases
Genome annotation databases
Family and domain databases
|InterPro||IPR002662. Birna_VP2. |
|Pfam||PF01766. Birna_VP2. 1 hit. |
PF01767. Birna_VP3. 1 hit.
PF01768. Birna_VP4. 1 hit.
|PROSITE||PS51548. BIRNAVIRUS_VP4_PRO. 1 hit. |
|Accession||Primary (citable) accession number: P05844|
Secondary accession number(s): Q82720
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Viral Protein Annotation Program|