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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).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
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

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-KW
  2. T=13 icosahedral viral capsid Source: UniProtKB-KW
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 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 – 9703Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MSTSKATATY LRSIMLPENG PASIPDDITE RHILKQETSS YNLEVSESGS
60 70 80 90 100
GLLVCFPGAP GSRVGAHYRW NLNQTALEFD QWLETSQDLK KAFNYGRLIS
110 120 130 140 150
RKYDIQSSTL PAGLYALNGT LNAATFEGSL SEVESLTYNS LMSLTTNPQD
160 170 180 190 200
KVNNQLVTKG ITVLNLPTGF DKPYVRLEDE TPQGPQSMNG ARMRCTAAIA
210 220 230 240 250
PRRYEIDLPS ERLPTVAATG TPTTIYEGNA DIVNSTAVTG DITFQLEAEP
260 270 280 290 300
VNETRFDFIL QFLGLDNDVP VVTVTSSTLV TADNYRGASA KFTQSIPTEM
310 320 330 340 350
ITKPITRVKL AYQLNQQTAI ANAATLGAKG PASVSFSSGN GNVPGVLRPI
360 370 380 390 400
TLVAYEKMTP QSILTVAGVS NYELIPNPDL LKNMVTKYGK YDPEGLNYAK
410 420 430 440 450
MILSHREELD IRTVWRTEEY KERTRAFKEI TDFTSDLPTS KAWGWRDLVR
460 470 480 490 500
GIRKVAAPVL STLFPMAAPL IGAADQFIGD LTKTNSAGGR YLSHAAGGRY
510 520 530 540 550
HDVMDSWASG SEAGSYSKHL KTRLESNNYE EVELPKPTKG VIFPVVHTVE
560 570 580 590 600
SAPGEAFGSL VVVIPEAYPE LLDPNQQVLS YFKNDTGCVW GIGEDIPFEG
610 620 630 640 650
DDMCYTALPL KEIKRNGNIV VEKIFAGPAM GPSSQLALSL LVNDIDEGIP
660 670 680 690 700
RMVFTGEIAD DEETVIPICG VDIKAIAAHE HGLPLIGCQP GVDEMVANTS
710 720 730 740 750
LASHLIQGGA LPVQKAQGAC RRIKYLGQLM RTTASGMDAE LQGLLQATMA
760 770 780 790 800
RAKEVKDAEV FKLLKLMSWT RKNDLTDHMY EWSKEDPDAI KFGRLVSTPP
810 820 830 840 850
KHQEKPKGPD QHTAQEAKAT RISLDAVKAG ADFASPEWIA ENNYRGPSPG
860 870 880 890 900
QFKYYMITGR VPNPGEEYED YVRKPITRPT DMDKIRRLAN SVYGLPHQEP
910 920 930 940 950
APDDFYQAVV EVFAENGGRG PDQDQMQDLR DLARQMKRRP RPAETRRQTK
960 970
TPPRAATSSG SRFTPSGDDG EV
Length:972
Mass (Da):106,666
Last modified:May 30, 2000 - v2
Checksum:i5CABCD0414EE122B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 80 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