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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)DescriptionActionsGraphical viewLength
Metal bindingi30Divalent metal cation; shared with trimeric partnersBy similarity1
Active sitei652NucleophilePROSITE-ProRule annotation1
Active sitei692PROSITE-ProRule annotation1

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)DescriptionActionsGraphical viewLength
ChainiPRO_00003783561 – 1012Structural polyproteinAdd BLAST1012
ChainiPRO_00003783571 – 512Precursor of VP2Add BLAST512
ChainiPRO_00000367761 – 441Capsid protein VP2Add BLAST441
PeptideiPRO_0000227849442 – 487Structural peptide 1By similarityAdd BLAST46
PeptideiPRO_0000227850488 – 494Structural peptide 2By similarity7
PeptideiPRO_0000227851495 – 501Structural peptide 3By similarity7
PeptideiPRO_0000227852502 – 512Structural peptide 4By similarityAdd BLAST11
ChainiPRO_0000227853513 – 755Protease VP4Add BLAST243
ChainiPRO_0000227854756 – 1012Capsid protein VP3Add BLAST257

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)DescriptionActionsGraphical viewLength
Sitei441 – 442Cleavage; by protease VP4By similarity2
Sitei487 – 488Cleavage; by protease VP4By similarity2
Sitei494 – 495Cleavage; by protease VP4By similarity2
Sitei501 – 502Cleavage; by protease VP4By similarity2
Sitei512 – 513Cleavage; by protease VP4By similarity2
Sitei755 – 756Cleavage; by protease VP4By similarity2

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

11012
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi13 – 19Combined sources7
Helixi21 – 23Combined sources3
Beta strandi36 – 48Combined sources13
Beta strandi51 – 53Combined sources3
Beta strandi55 – 59Combined sources5
Beta strandi64 – 74Combined sources11
Beta strandi80 – 87Combined sources8
Helixi92 – 94Combined sources3
Beta strandi96 – 110Combined sources15
Beta strandi123 – 131Combined sources9
Helixi133 – 135Combined sources3
Helixi143 – 146Combined sources4
Helixi151 – 153Combined sources3
Beta strandi154 – 159Combined sources6
Turni160 – 162Combined sources3
Beta strandi164 – 167Combined sources4
Beta strandi204 – 218Combined sources15
Beta strandi225 – 238Combined sources14
Beta strandi240 – 249Combined sources10
Beta strandi255 – 265Combined sources11
Beta strandi270 – 277Combined sources8
Beta strandi288 – 296Combined sources9
Helixi298 – 300Combined sources3
Beta strandi305 – 318Combined sources14
Beta strandi325 – 337Combined sources13
Turni338 – 341Combined sources4
Turni343 – 345Combined sources3
Beta strandi349 – 356Combined sources8
Beta strandi362 – 375Combined sources14
Helixi379 – 381Combined sources3
Helixi394 – 403Combined sources10
Helixi405 – 408Combined sources4
Beta strandi412 – 415Combined sources4
Helixi416 – 425Combined sources10
Turni434 – 438Combined sources5
Helixi444 – 454Combined sources11
Helixi456 – 462Combined sources7
Helixi468 – 474Combined sources7
Helixi476 – 481Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61825.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini513 – 755Peptidase S50PROSITE-ProRule annotationAdd BLAST243

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1003 – 1012Interaction with VP1 protein10

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)DescriptionActionsGraphical viewLength
Natural varianti80Y → L in strain: Isolate Indian. 1
Natural varianti253H → Q in strain: Isolate Indian. 1
Natural varianti263L → F in strain: Isolate Indian. 1
Natural varianti270A → T in strain: Isolate Indian. 1
Natural varianti279N → D in strain: Isolate Indian. 1
Natural varianti284T → A in strain: Isolate Indian. 1
Natural varianti290L → M in strain: Isolate Indian. 1
Natural varianti312I → V in strain: Isolate Indian. 1
Natural varianti330R → S in strain: Isolate Indian. 1
Natural varianti409G → A in strain: Isolate Indian. 1

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
PDB 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.
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: November 2, 2016
This is version 68 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.