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Protein

Structural polyprotein

Gene
N/A
Organism
Infectious pancreatic necrosis virus (strain Jasper) (IPNV)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Metal bindingi26Divalent metal cation; shared with trimeric partners1
Active sitei633NucleophilePROSITE-ProRule annotation1
Active sitei674PROSITE-ProRule annotation1

GO - Molecular functioni

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]
Proteomesi
  • UP000007248 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003916321 – 972Structural polyproteinAdd BLAST972
ChainiPRO_00003916331 – 508Precursor of VP2Add BLAST508
ChainiPRO_00000367801 – 442Capsid protein VP2Add BLAST442
PeptideiPRO_0000227859443 – 486Structural peptide 1By similarityAdd BLAST44
PeptideiPRO_0000227860487 – 495Structural peptide 2By similarity9
PeptideiPRO_0000227861496 – 508Structural peptide 3By similarityAdd BLAST13
ChainiPRO_0000036781509 – 734Protease VP4Add BLAST226
ChainiPRO_0000036782735 – 972Capsid protein VP3Add BLAST238

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.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei442 – 443Cleavage; by protease VP4By similarity2
Sitei486 – 487Cleavage; by protease VP4By similarity2
Sitei495 – 496Cleavage; by protease VP4By similarity2
Sitei508 – 509Cleavage; by protease VP4By similarity2
Sitei734 – 735Cleavage; by protease VP4By similarity2

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

1972
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi968 – 970Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZEDX-ray2.20D/E/F735-972[»]
ProteinModelPortaliP05844.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini509 – 734Peptidase S50PROSITE-ProRule annotationAdd BLAST226

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.
KEGGivg:956513.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZEDX-ray2.20D/E/F735-972[»]
ProteinModelPortaliP05844.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi956513.
KEGGivg:956513.

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]
ProtoNetiSearch...

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 5, 2016
This is version 86 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.