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Protein

Structural polyprotein

Gene
N/A
Organism
Avian infectious bursal disease virus (IBDV) (Gumboro disease virus)
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 by interacting with host ITGA4/ITGB1 (By similarity).By similarity
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 made 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 pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry.
Structural peptide 2 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity).By similarity
Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity).By similarity
Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi30 – 301Divalent metal cation; shared with trimeric partnersBy similarity
Active sitei652 – 6521NucleophilePROSITE-ProRule annotation
Active sitei692 – 6921PROSITE-ProRule annotation

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Keywords - Ligandi

Metal-binding

Protein family/group databases

TCDBi1.A.59.1.1. the bursal disease virus pore-forming peptide, pep46 (pep46) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Structural polyprotein
Short name:
PP
Cleaved into the following 8 chains:
Precursor of VP2
Short name:
Pre-VP2
Structural peptide 1
Short name:
p1
Alternative name(s):
pep46
Structural peptide 2
Short name:
p2
Alternative name(s):
pep7a
Structural peptide 3
Short name:
p3
Alternative name(s):
pep7b
Structural peptide 4
Short name:
p4
Alternative name(s):
pep11
Alternative name(s):
Non-structural protein VP4
Short name:
NS
OrganismiAvian infectious bursal disease virus (IBDV) (Gumboro disease virus)
Taxonomic identifieri10995 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesBirnaviridaeAvibirnavirus
Virus hostiGallus gallus (Chicken) [TaxID: 9031]
Meleagris gallopavo (Common turkey) [TaxID: 9103]

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10121012Structural polyproteinPRO_0000378356Add
BLAST
Chaini1 – 512512Precursor of VP2PRO_0000378357Add
BLAST
Chaini1 – 441441Capsid protein VP2PRO_0000036776Add
BLAST
Peptidei442 – 48746Structural peptide 1By similarityPRO_0000227849Add
BLAST
Peptidei488 – 4947Structural peptide 2By similarityPRO_0000227850
Peptidei495 – 5017Structural peptide 3By similarityPRO_0000227851
Peptidei502 – 51211Structural peptide 4By similarityPRO_0000227852Add
BLAST
Chaini513 – 755243Protease VP4PRO_0000227853Add
BLAST
Chaini756 – 1012257Capsid protein VP3PRO_0000227854Add
BLAST

Post-translational modificationi

Specific enzymatic cleavages yield mature proteins. The 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 (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei441 – 4422Cleavage; by protease VP4By similarity
Sitei487 – 4882Cleavage; by protease VP4By similarity
Sitei494 – 4952Cleavage; by protease VP4By similarity
Sitei501 – 5022Cleavage; by protease VP4By similarity
Sitei512 – 5132Cleavage; by protease VP4By similarity
Sitei755 – 7562Cleavage; by protease VP4By similarity

Interactioni

Subunit structurei

Capsid protein VP2 is a homotrimer. A central divalent metal stabilizes the VP2 trimer, possibly calcium. Capsid protein VP3 is a homodimer. Capsid protein VP2 interacts with host ITGA4/ITGB1. Capsid protein VP3 interacts (via C-terminus) with VP1 in the cytoplasm. Capsid VP3 interacts with VP2 (By similarity).By similarity

Protein-protein interaction databases

DIPiDIP-29594N.

Structurei

Secondary structure

1
1012
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 197Combined sources
Helixi21 – 233Combined sources
Beta strandi36 – 4813Combined sources
Beta strandi51 – 533Combined sources
Beta strandi55 – 595Combined sources
Beta strandi64 – 7411Combined sources
Beta strandi80 – 878Combined sources
Helixi92 – 943Combined sources
Beta strandi96 – 11015Combined sources
Beta strandi123 – 1319Combined sources
Helixi133 – 1353Combined sources
Helixi143 – 1464Combined sources
Helixi151 – 1533Combined sources
Beta strandi154 – 1596Combined sources
Turni160 – 1623Combined sources
Beta strandi164 – 1674Combined sources
Beta strandi204 – 21815Combined sources
Beta strandi225 – 23814Combined sources
Beta strandi240 – 24910Combined sources
Beta strandi255 – 26511Combined sources
Beta strandi270 – 2778Combined sources
Beta strandi288 – 2969Combined sources
Helixi298 – 3003Combined sources
Beta strandi305 – 31814Combined sources
Beta strandi325 – 33713Combined sources
Turni338 – 3414Combined sources
Turni343 – 3453Combined sources
Beta strandi349 – 3568Combined sources
Beta strandi362 – 37514Combined sources
Helixi379 – 3813Combined sources
Helixi394 – 40310Combined sources
Helixi405 – 4084Combined sources
Beta strandi412 – 4154Combined sources
Helixi416 – 42510Combined sources
Turni434 – 4385Combined sources
Helixi444 – 45411Combined sources
Helixi456 – 4627Combined sources
Helixi468 – 4747Combined sources
Helixi476 – 4816Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2GSYX-ray2.60A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T1-456[»]
2IMUNMR-A442-487[»]
3FBMX-ray3.10A6-452[»]
ProteinModelPortaliP61825.
SMRiP61825. Positions 8-440, 442-487, 846-974.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61825.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini513 – 755243Peptidase S50PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1003 – 101210Interaction with VP1 protein

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.

P61825-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTNLQDQTQQ IVPFIRSLLM PTTGPASIPD DTLEKHTLRS ETSTYNLTVG
60 70 80 90 100
DTGSGLIVFF PGFPGSIVGA HYTLQSNGNY KFDQMLLTAQ NLPASYNYCR
110 120 130 140 150
LVSRSLTVRS STLPGGVYAL NGTINAVTFQ GSLSELTDVS YNGLMSATAN
160 170 180 190 200
INDKIGNVLV GEGVTVLSLP TSYDLGYVRL GDPIPAIGLD PKMVATCDSS
210 220 230 240 250
DRPRVYTITA ADDYQFSSQY QPGGVTITLF SANIDAITSL SVGGELVFQT
260 270 280 290 300
SVHGLVLGAT IYLIGFDGTA VITRAVAANN GLTTGTDNLL PFNLVIPTNE
310 320 330 340 350
ITQPITSIKL EIVTSKSGGQ AGDQMSWSAR GSLAVTIHGG NYPGALRPVT
360 370 380 390 400
LVAYERVATG SVVTVAGVSN FELIPNPELA KNLVTEYGRF DPGAMNYTKL
410 420 430 440 450
ILSERDRLGI KTVWPTREYT DFREYFMEVA DLNSPLKIAG AFGFKDIIRA
460 470 480 490 500
IRRIAVPVVS TLFPPAAPLA HAIGEGVDYL LGDEAQAASG TARAASGKAR
510 520 530 540 550
AASGRIRQLT LAADKGYEVV ANLFQVPQNP VVDGILASPG VLRGAHNLDC
560 570 580 590 600
VLREGATLFP VVITTVEDAM TPKALNSKMF AVIEGVREDL QPPSQRGSFI
610 620 630 640 650
RTLSGHRVYG YAPDGVLPLE TGRDYTVVPI DDVWDDSIML SKDPIPPIVG
660 670 680 690 700
NSGNLAIAYM DVFRPKVPIH VAMTGALNAC GEIEKVSFRS TKLATAHRLG
710 720 730 740 750
LKLAGPGAFD VNTGPNWATF IKRFPHNPRD WDRLPYLNLP YLPPNAGRQY
760 770 780 790 800
HLAMAASEFK ETPELESAVR AMEAAANVDP LFQSALSVFM WLEENGIVTD
810 820 830 840 850
MANFALSDPN AHRMRNFLAN APQAGSKSQR AKYGTAGYGV EARGPTPEEA
860 870 880 890 900
QREKDTRISK KMETMGIYFA TPEWVALNGH RGPSPGQLKY WQNTREIPDP
910 920 930 940 950
NEDYLDYVHA EKSRLASEEQ ILRAATSIYG APGQAEPPQA FIDEVAKVYE
960 970 980 990 1000
INHGRGPNQE QMKDLLLTAM EMKHRNPRRA LPKPKPKPNA PTQRPPGRLG
1010
RWIRTVSDED LE
Length:1,012
Mass (Da):109,671
Last modified:April 4, 2006 - v2
Checksum:i1C58BCEB0FDB9EE1
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti80 – 801Y → L in strain: Isolate Indian.
Natural varianti253 – 2531H → Q in strain: Isolate Indian.
Natural varianti263 – 2631L → F in strain: Isolate Indian.
Natural varianti270 – 2701A → T in strain: Isolate Indian.
Natural varianti279 – 2791N → D in strain: Isolate Indian.
Natural varianti284 – 2841T → A in strain: Isolate Indian.
Natural varianti290 – 2901L → M in strain: Isolate Indian.
Natural varianti312 – 3121I → V in strain: Isolate Indian.
Natural varianti330 – 3301R → S in strain: Isolate Indian.
Natural varianti409 – 4091G → A in strain: Isolate Indian.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF194428 mRNA. Translation: AAF16082.1.
AJ621158 Genomic RNA. Translation: CAF18300.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF194428 mRNA. Translation: AAF16082.1.
AJ621158 Genomic RNA. Translation: CAF18300.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2GSYX-ray2.60A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T1-456[»]
2IMUNMR-A442-487[»]
3FBMX-ray3.10A6-452[»]
ProteinModelPortaliP61825.
SMRiP61825. Positions 8-440, 442-487, 846-974.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-29594N.

Protein family/group databases

TCDBi1.A.59.1.1. the bursal disease virus pore-forming peptide, pep46 (pep46) family.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP61825.

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_IBDV
AccessioniPrimary (citable) accession number: P61825
Secondary accession number(s): Q9Q6Q6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: April 4, 2006
Last modified: December 9, 2015
This is version 66 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

The sequence shown is that of isolate CEF94.

Keywords - Technical termi

3D-structure

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.