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P05844

- POLS_IPNVJ

UniProt

P05844 - POLS_IPNVJ

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
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    • History
      Entry version 78 (01 Oct 2014)
      Sequence version 2 (30 May 2000)
      Previous versions | rss
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    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.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 annotation
    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.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.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.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.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi26 – 261Divalent metal cation; shared with trimeric partners
    Sitei442 – 4432Cleavage; by protease VP4By similarity
    Sitei486 – 4872Cleavage; by protease VP4By similarity
    Sitei495 – 4962Cleavage; by protease VP4By similarity
    Sitei508 – 5092Cleavage; by protease VP4By similarity
    Active sitei633 – 6331NucleophilePROSITE-ProRule annotation
    Active sitei674 – 6741PROSITE-ProRule annotation
    Sitei734 – 7352Cleavage; by protease VP4By 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

    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

    GO - Cellular componenti

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

    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 polyproteinPRO_0000391632Add
    BLAST
    Chaini1 – 508508Precursor of VP2PRO_0000391633Add
    BLAST
    Chaini1 – 442442Capsid protein VP2PRO_0000036780Add
    BLAST
    Peptidei443 – 48644Structural peptide 1By similarityPRO_0000227859Add
    BLAST
    Peptidei487 – 4959Structural peptide 2By similarityPRO_0000227860
    Peptidei496 – 50813Structural peptide 3By similarityPRO_0000227861Add
    BLAST
    Chaini509 – 734226Protease VP4PRO_0000036781Add
    BLAST
    Chaini735 – 972238Capsid protein VP3PRO_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.By similarity

    Structurei

    Secondary structure

    1
    972
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini509 – 734226Peptidase S50PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 peptidase S50 domain.PROSITE-ProRule annotation

    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

    « Hide

    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: October 1, 2014
    This is version 78 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