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P05844

- POLS_IPNVJ

UniProt

P05844 - POLS_IPNVJ

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Protein
Structural polyprotein
Gene
N/A
Organism
Infectious pancreatic necrosis virus (strain Jasper) (IPNV)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi26 – 261Divalent metal cation; shared with trimeric partners
Sitei442 – 4432Cleavage; by protease VP4 By similarity
Sitei486 – 4872Cleavage; by protease VP4 By similarity
Sitei495 – 4962Cleavage; by protease VP4 By similarity
Sitei508 – 5092Cleavage; by protease VP4 By similarity
Active sitei633 – 6331Nucleophile By similarity
Active sitei674 – 6741 By similarity
Sitei734 – 7352Cleavage; by protease VP4 By similarity

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. serine-type peptidase activity Source: UniProtKB-KW
  3. structural molecule activity Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Keywords - Ligandi

Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Structural polyprotein
Short name:
PP
Cleaved into the following 7 chains:
Precursor of VP2
Short name:
Pre-VP2
Structural peptide 1
Short name:
p1
Structural peptide 2
Short name:
p2
Structural peptide 3
Short name:
p3
Alternative name(s):
Non-structural protein VP4
Short name:
NS
OrganismiInfectious pancreatic necrosis virus (strain Jasper) (IPNV)
Taxonomic identifieri11003 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesBirnaviridaeAquabirnavirus
Virus hostiOncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) [TaxID: 8022]
Salmo [TaxID: 8028]
ProteomesiUP000007248: Genome

Subcellular locationi

Chain Capsid protein VP2 : Virion Reviewed prediction. Host cytoplasm Reviewed prediction
Chain Capsid protein VP3 : Virion Reviewed prediction. Host cytoplasm Reviewed prediction
Structural peptide 1 : Virion Reviewed prediction. Host cytoplasm Reviewed prediction
Structural peptide 2 : Virion Reviewed prediction. Host cytoplasm Reviewed prediction
Structural peptide 3 : Virion Reviewed prediction. Host cytoplasm Reviewed prediction

GO - Cellular componenti

  1. T=13 icosahedral viral capsid Source: UniProtKB-KW
  2. host cell cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, T=13 icosahedral capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 972972Structural polyprotein
PRO_0000391632Add
BLAST
Chaini1 – 508508Precursor of VP2
PRO_0000391633Add
BLAST
Chaini1 – 442442Capsid protein VP2
PRO_0000036780Add
BLAST
Peptidei443 – 48644Structural peptide 1 By similarity
PRO_0000227859Add
BLAST
Peptidei487 – 4959Structural peptide 2 By similarity
PRO_0000227860
Peptidei496 – 50813Structural peptide 3 By similarity
PRO_0000227861Add
BLAST
Chaini509 – 734226Protease VP4
PRO_0000036781Add
BLAST
Chaini735 – 972238Capsid protein VP3
PRO_0000036782Add
BLAST

Post-translational modificationi

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.

Interactioni

Subunit structurei

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.1 Publication

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi968 – 9703

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZEDX-ray2.20D/E/F735-972[»]
ProteinModelPortaliP05844.
SMRiP05844. Positions 514-716.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini509 – 734226Peptidase S50
Add
BLAST

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.20. 2 hits.
InterProiIPR002662. Birna_VP2.
IPR002663. Birna_VP3.
IPR025775. Birna_VP4_Prtase_dom.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF01766. Birna_VP2. 1 hit.
PF01767. Birna_VP3. 1 hit.
PF01768. Birna_VP4. 1 hit.
[Graphical view]
PROSITEiPS51548. BIRNAVIRUS_VP4_PRO. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P05844-1 [UniParc]FASTAAdd to Basket

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MSTSKATATY LRSIMLPENG PASIPDDITE RHILKQETSS YNLEVSESGS    50
GLLVCFPGAP GSRVGAHYRW NLNQTALEFD QWLETSQDLK KAFNYGRLIS 100
RKYDIQSSTL PAGLYALNGT LNAATFEGSL SEVESLTYNS LMSLTTNPQD 150
KVNNQLVTKG ITVLNLPTGF DKPYVRLEDE TPQGPQSMNG ARMRCTAAIA 200
PRRYEIDLPS ERLPTVAATG TPTTIYEGNA DIVNSTAVTG DITFQLEAEP 250
VNETRFDFIL QFLGLDNDVP VVTVTSSTLV TADNYRGASA KFTQSIPTEM 300
ITKPITRVKL AYQLNQQTAI ANAATLGAKG PASVSFSSGN GNVPGVLRPI 350
TLVAYEKMTP QSILTVAGVS NYELIPNPDL LKNMVTKYGK YDPEGLNYAK 400
MILSHREELD IRTVWRTEEY KERTRAFKEI TDFTSDLPTS KAWGWRDLVR 450
GIRKVAAPVL STLFPMAAPL IGAADQFIGD LTKTNSAGGR YLSHAAGGRY 500
HDVMDSWASG SEAGSYSKHL KTRLESNNYE EVELPKPTKG VIFPVVHTVE 550
SAPGEAFGSL VVVIPEAYPE LLDPNQQVLS YFKNDTGCVW GIGEDIPFEG 600
DDMCYTALPL KEIKRNGNIV VEKIFAGPAM GPSSQLALSL LVNDIDEGIP 650
RMVFTGEIAD DEETVIPICG VDIKAIAAHE HGLPLIGCQP GVDEMVANTS 700
LASHLIQGGA LPVQKAQGAC RRIKYLGQLM RTTASGMDAE LQGLLQATMA 750
RAKEVKDAEV FKLLKLMSWT RKNDLTDHMY EWSKEDPDAI KFGRLVSTPP 800
KHQEKPKGPD QHTAQEAKAT RISLDAVKAG ADFASPEWIA ENNYRGPSPG 850
QFKYYMITGR VPNPGEEYED YVRKPITRPT DMDKIRRLAN SVYGLPHQEP 900
APDDFYQAVV EVFAENGGRG PDQDQMQDLR DLARQMKRRP RPAETRRQTK 950
TPPRAATSSG SRFTPSGDDG EV 972
Length:972
Mass (Da):106,666
Last modified:May 30, 2000 - v2
Checksum:i5CABCD0414EE122B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M18049 Genomic RNA. Translation: AAA89179.1.
PIRiA23599. GNXSIV.
T09624.
RefSeqiNP_047196.1. NC_001915.1.

Genome annotation databases

GeneIDi956513.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M18049 Genomic RNA. Translation: AAA89179.1 .
PIRi A23599. GNXSIV.
T09624.
RefSeqi NP_047196.1. NC_001915.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3ZED X-ray 2.20 D/E/F 735-972 [» ]
ProteinModelPortali P05844.
SMRi P05844. Positions 514-716.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 956513.

Family and domain databases

Gene3Di 2.60.120.20. 2 hits.
InterProi IPR002662. Birna_VP2.
IPR002663. Birna_VP3.
IPR025775. Birna_VP4_Prtase_dom.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF01766. Birna_VP2. 1 hit.
PF01767. Birna_VP3. 1 hit.
PF01768. Birna_VP4. 1 hit.
[Graphical view ]
PROSITEi PS51548. BIRNAVIRUS_VP4_PRO. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "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].
  2. "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.
  3. "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.

Entry informationi

Entry nameiPOLS_IPNVJ
AccessioniPrimary (citable) accession number: P05844
Secondary accession number(s): Q82720
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: May 30, 2000
Last modified: July 9, 2014
This is version 77 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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