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Structural polyprotein (PP) [Cleaved into: Precursor of VP2 (Pre-VP2); Capsid protein VP2; Structural peptide 1 (p1) (pep46); Structural peptide 2 (p2) (pep7a); Structural peptide 3 (p3) (pep7b); Structural peptide 4 (p4) (pep11); Protease VP4 (EC 3.4.21.-) (Non-structural protein VP4) (NS); Capsid protein VP3]

 POLS_IBDVC              Reviewed;        1012 AA.
P15480;
01-APR-1990, integrated into UniProtKB/Swiss-Prot.
01-APR-1990, sequence version 1.
10-MAY-2017, entry version 94.
RecName: Full=Structural polyprotein;
Short=PP;
Contains:
RecName: Full=Precursor of VP2;
Short=Pre-VP2;
Contains:
RecName: Full=Capsid protein VP2;
Contains:
RecName: Full=Structural peptide 1;
Short=p1;
AltName: Full=pep46;
Contains:
RecName: Full=Structural peptide 2;
Short=p2;
AltName: Full=pep7a;
Contains:
RecName: Full=Structural peptide 3;
Short=p3;
AltName: Full=pep7b;
Contains:
RecName: Full=Structural peptide 4;
Short=p4;
AltName: Full=pep11;
Contains:
RecName: Full=Protease VP4;
EC=3.4.21.-;
AltName: Full=Non-structural protein VP4;
Short=NS;
Contains:
RecName: Full=Capsid protein VP3;
Avian infectious bursal disease virus (strain Cu-1) (IBDV) (Gumboro
disease virus).
Viruses; dsRNA viruses; Birnaviridae; Avibirnavirus.
NCBI_TaxID=10998;
NCBI_TaxID=9031; Gallus gallus (Chicken).
NCBI_TaxID=9103; Meleagris gallopavo (Common turkey).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
PubMed=2552417; DOI=10.1093/nar/17.19.7982;
Spies U., Mueller H., Becht H.;
"Nucleotide sequence of infectious bursal disease virus genome segment
A delineates two major open reading frames.";
Nucleic Acids Res. 17:7982-7982(1989).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
PubMed=2161902; DOI=10.1099/0022-1317-71-6-1303;
Bayliss C.D., Spies U., Shaw K., Peters R.W., Papageorgiou A.,
Mueller H., Boursnell M.E.G.;
"A comparison of the sequences of segment A of four infectious bursal
disease virus strains and identification of a variable region in
VP2.";
J. Gen. Virol. 71:1303-1312(1990).
[3]
PROTEIN SEQUENCE OF 513-519 AND 756-762, ACTIVE SITES OF PROTEASE VP4,
PROTEOLYTIC PROCESSING OF POLYPROTEIN, AND MUTAGENESIS OF
487-ALA-ALA-488; 495-ALA-ALA-494; 501-ALA-ALA-502; 512-ALA-ALA-513;
SER-652; LYS-692 AND 755-ALA-ALA-756.
STRAIN=Isolate vaccine CT;
PubMed=10725424;
Lejal N., Da Costa B., Huet J.-C., Delmas B.;
"Role of Ser-652 and Lys-692 in the protease activity of infectious
bursal disease virus VP4 and identification of its substrate cleavage
sites.";
J. Gen. Virol. 81:983-992(2000).
[4]
PROTEIN SEQUENCE OF 442-456 AND 488-512, PROTEOLYTIC PROCESSING OF
POLYPROTEIN, AND MUTAGENESIS OF ALA-441; PHE-442; 487-ALA-ALA-488;
494-ALA-ALA-495; 501-ALA-ALA-502; ALA-512 AND ALA-513.
STRAIN=Isolate vaccine CT;
PubMed=11836417; DOI=10.1128/jvi.76.5.2393-2402.2002;
Da Costa B., Chevalier C., Henry C., Huet J.-C., Petit S., Lepault J.,
Boot H., Delmas B.;
"The capsid of infectious bursal disease virus contains several small
peptides arising from the maturation process of pVP2.";
J. Virol. 76:2393-2402(2002).
[5]
3D-STRUCTURE MODELING, AND ELECTRON MICROSCOPY (15 ANGSTROMS) OF VIRAL
PARTICLES.
STRAIN=Isolate vaccine CT;
PubMed=16033982; DOI=10.1099/vir.0.80942-0;
Pous J., Chevalier C., Ouldali M., Navaza J., Delmas B., Lepault J.;
"Structure of birnavirus-like particles determined by combined
electron cryomicroscopy and X-ray crystallography.";
J. Gen. Virol. 86:2339-2346(2005).
[6]
X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 1-441.
PubMed=15797378; DOI=10.1016/j.cell.2005.01.009;
Coulibaly F., Chevalier C., Gutsche I., Pous J., Navaza J.,
Bressanelli S., Delmas B., Rey F.A.;
"The birnavirus crystal structure reveals structural relationships
among icosahedral viruses.";
Cell 120:761-772(2005).
-!- FUNCTION: 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).
{ECO:0000250}.
-!- FUNCTION: 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).
{ECO:0000250}.
-!- FUNCTION: 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. {ECO:0000255|PROSITE-ProRule:PRU00881}.
-!- FUNCTION: 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). {ECO:0000250}.
-!- FUNCTION: Structural peptide 1 is a small peptide derived from
pre-VP2 C-terminus. It destabilizes and perforates cell membranes,
suggesting a role during entry (By similarity). {ECO:0000250}.
-!- FUNCTION: Structural peptide 2 is a small peptide derived from
pVP2 C-terminus. It is not essential for the virus viability, but
viral growth is affected when missing.
-!- FUNCTION: Structural peptide 3 is a small peptide derived from
pVP2 C-terminus. It is not essential for the virus viability, but
viral growth is affected when missing.
-!- FUNCTION: Structural peptide 4 is a small peptide derived from
pVP2 C-terminus. It is essential for the virus viability.
-!- SUBUNIT: Capsid protein VP2 is a homotrimer. A central divalent
metal stabilizes the VP2 trimer, possibly calcium (By similarity).
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). {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Capsid protein VP2: Virion {ECO:0000305}.
Host cytoplasm {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Capsid protein VP3: Virion {ECO:0000305}.
Host cytoplasm {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Structural peptide 1: Virion {ECO:0000305}.
Host cytoplasm {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Structural peptide 2: Virion {ECO:0000305}.
Host cytoplasm {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Structural peptide 3: Virion {ECO:0000305}.
Host cytoplasm {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Structural peptide 4: Virion {ECO:0000305}.
Host cytoplasm {ECO:0000305}.
-!- PTM: 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). {ECO:0000250}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; X16107; CAA34234.1; -; Genomic_RNA.
EMBL; D00867; BAA00740.1; -; Genomic_RNA.
PIR; A35353; GNXSCU.
PDB; 1WCD; X-ray; 3.00 A; J=1-441.
PDB; 1WCE; X-ray; 7.00 A; A/B/C/D/E/F/G/H/I/J/K/L/M=1-441.
PDBsum; 1WCD; -.
PDBsum; 1WCE; -.
ProteinModelPortal; P15480; -.
SMR; P15480; -.
EvolutionaryTrace; P15480; -.
GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0039621; C:T=13 icosahedral viral capsid; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008236; F:serine-type peptidase activity; IEA:UniProtKB-KW.
GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
InterPro; IPR002662; Birna_VP2.
InterPro; IPR002663; Birna_VP3.
InterPro; IPR025775; Birna_VP4_Prtase_dom.
Pfam; PF01766; Birna_VP2; 1.
Pfam; PF01767; Birna_VP3; 1.
Pfam; PF01768; Birna_VP4; 1.
PROSITE; PS51548; BIRNAVIRUS_VP4_PRO; 1.
1: Evidence at protein level;
3D-structure; Capsid protein; Direct protein sequencing;
Host cytoplasm; Hydrolase; Metal-binding; Protease; Serine protease;
T=13 icosahedral capsid protein; Virion.
CHAIN 1 1012 Structural polyprotein.
/FTId=PRO_0000392588.
CHAIN 1 512 Precursor of VP2.
/FTId=PRO_0000392589.
CHAIN 1 441 Capsid protein VP2.
/FTId=PRO_0000036765.
PEPTIDE 442 487 Structural peptide 1.
{ECO:0000269|PubMed:11836417}.
/FTId=PRO_0000227831.
PEPTIDE 488 494 Structural peptide 2.
/FTId=PRO_0000227832.
PEPTIDE 495 501 Structural peptide 3.
/FTId=PRO_0000227833.
PEPTIDE 502 512 Structural peptide 4.
{ECO:0000269|PubMed:10725424}.
/FTId=PRO_0000227834.
CHAIN 513 755 Protease VP4.
/FTId=PRO_0000036766.
CHAIN 756 1012 Capsid protein VP3.
/FTId=PRO_0000036767.
DOMAIN 513 755 Peptidase S50. {ECO:0000255|PROSITE-
ProRule:PRU00881}.
REGION 1003 1012 Interaction with VP1 protein.
{ECO:0000250}.
ACT_SITE 652 652 Nucleophile. {ECO:0000255|PROSITE-
ProRule:PRU00881,
ECO:0000269|PubMed:10725424}.
ACT_SITE 692 692 {ECO:0000255|PROSITE-ProRule:PRU00881,
ECO:0000269|PubMed:10725424}.
METAL 30 30 Divalent metal cation; shared with
trimeric partners. {ECO:0000250}.
SITE 441 442 Cleavage; by protease VP4.
SITE 487 488 Cleavage; by protease VP4.
SITE 494 495 Cleavage; by protease VP4.
SITE 501 502 Cleavage; by protease VP4.
SITE 512 513 Cleavage; by protease VP4.
SITE 755 756 Cleavage; by protease VP4.
MUTAGEN 441 441 A->E,Q,R: Lethal for the virus.
{ECO:0000269|PubMed:11836417}.
MUTAGEN 442 442 F->D,G,N: Lethal for the virus.
{ECO:0000269|PubMed:11836417}.
MUTAGEN 487 488 AA->EF: No effect on virus growth.
{ECO:0000269|PubMed:10725424,
ECO:0000269|PubMed:11836417}.
MUTAGEN 487 488 AA->QL: No effect on polyprotein
processing. {ECO:0000269|PubMed:10725424,
ECO:0000269|PubMed:11836417}.
MUTAGEN 494 495 AA->EF: 80% reduction of virus growth,
small-plaque phenotype.
{ECO:0000269|PubMed:10725424,
ECO:0000269|PubMed:11836417}.
MUTAGEN 494 495 AA->QL: No effect on polyprotein
processing. {ECO:0000269|PubMed:10725424,
ECO:0000269|PubMed:11836417}.
MUTAGEN 501 502 AA->EF: No effect on virus growth.
{ECO:0000269|PubMed:10725424,
ECO:0000269|PubMed:11836417}.
MUTAGEN 501 502 AA->QL: No effect on polyprotein
processing. {ECO:0000269|PubMed:10725424,
ECO:0000269|PubMed:11836417}.
MUTAGEN 512 513 AA->EF: Gives rise to uncleaved pVP2-VP4
and two shorter forms of VP2. Lethal for
the virus. {ECO:0000269|PubMed:10725424}.
MUTAGEN 512 512 A->D,L,N,V: Lethal for the virus.
{ECO:0000269|PubMed:11836417}.
MUTAGEN 512 512 A->G: Smaller amounts of cleaved forms of
pVP2. No effect virus growth.
{ECO:0000269|PubMed:11836417}.
MUTAGEN 512 512 A->I,L,N,R,S,V: Lethal for the virus.
{ECO:0000269|PubMed:11836417}.
MUTAGEN 513 513 A->G: No effect on polyprotein processing
and virus growth.
{ECO:0000269|PubMed:11836417}.
MUTAGEN 652 652 S->A,T: Complete loss of polyprotein
processing.
{ECO:0000269|PubMed:10725424}.
MUTAGEN 652 652 S->C: Partial loss of polyprotein
processing.
{ECO:0000269|PubMed:10725424}.
MUTAGEN 692 692 K->A,R,H: Complete loss of polyprotein
processing.
{ECO:0000269|PubMed:10725424}.
MUTAGEN 755 756 AA->EF: Gives rise to pVP2 and uncleaved
VP3-VP4. {ECO:0000269|PubMed:10725424}.
HELIX 14 19 {ECO:0000244|PDB:1WCD}.
HELIX 21 23 {ECO:0000244|PDB:1WCD}.
STRAND 36 48 {ECO:0000244|PDB:1WCD}.
STRAND 55 59 {ECO:0000244|PDB:1WCD}.
STRAND 64 74 {ECO:0000244|PDB:1WCD}.
STRAND 80 87 {ECO:0000244|PDB:1WCD}.
HELIX 92 94 {ECO:0000244|PDB:1WCD}.
STRAND 96 110 {ECO:0000244|PDB:1WCD}.
STRAND 123 131 {ECO:0000244|PDB:1WCD}.
HELIX 133 135 {ECO:0000244|PDB:1WCD}.
TURN 141 143 {ECO:0000244|PDB:1WCD}.
HELIX 144 146 {ECO:0000244|PDB:1WCD}.
HELIX 151 153 {ECO:0000244|PDB:1WCD}.
STRAND 154 159 {ECO:0000244|PDB:1WCD}.
TURN 160 162 {ECO:0000244|PDB:1WCD}.
STRAND 164 167 {ECO:0000244|PDB:1WCD}.
STRAND 204 218 {ECO:0000244|PDB:1WCD}.
STRAND 225 238 {ECO:0000244|PDB:1WCD}.
STRAND 240 249 {ECO:0000244|PDB:1WCD}.
STRAND 251 265 {ECO:0000244|PDB:1WCD}.
STRAND 270 282 {ECO:0000244|PDB:1WCD}.
STRAND 284 286 {ECO:0000244|PDB:1WCD}.
STRAND 288 293 {ECO:0000244|PDB:1WCD}.
HELIX 298 300 {ECO:0000244|PDB:1WCD}.
STRAND 305 314 {ECO:0000244|PDB:1WCD}.
STRAND 316 318 {ECO:0000244|PDB:1WCD}.
STRAND 325 337 {ECO:0000244|PDB:1WCD}.
TURN 338 341 {ECO:0000244|PDB:1WCD}.
STRAND 345 347 {ECO:0000244|PDB:1WCD}.
STRAND 349 356 {ECO:0000244|PDB:1WCD}.
STRAND 362 375 {ECO:0000244|PDB:1WCD}.
HELIX 379 381 {ECO:0000244|PDB:1WCD}.
HELIX 394 403 {ECO:0000244|PDB:1WCD}.
TURN 404 409 {ECO:0000244|PDB:1WCD}.
STRAND 412 415 {ECO:0000244|PDB:1WCD}.
HELIX 416 422 {ECO:0000244|PDB:1WCD}.
TURN 423 427 {ECO:0000244|PDB:1WCD}.
SEQUENCE 1012 AA; 109681 MW; 68C3941443013FBE CRC64;
MTNLQDQTQQ IVPFIRSLLM PTTGPASIPD DTLEKHTLRS ETSTYNLTVG DTGSGLIVFF
PGFPGSIVGA HYTLQSNGNY KFDQMLLTAQ NLPASYNYCR LVSRSLTVRS STLPGGVYAL
NGTINAVTFQ GSLSELTDVS YNGLMSATAN INDKIGNVLV GEGVTVLSLP TSYDLGYVRL
GDPIPAIGLD PKMVATCDSS DRPRVYTITA ADDYQFSSQY QPGGVTITLF SANIDAITSL
SVGGELVFQT SVHGLVLGAT IYLIGFDGTT VITRAVAANN GLTTGTDNLM PFNLVISTNE
ITQPITSIKL EIVTSKSGGQ AGDQMSWSAK GSLAVTIHGG NYPGALRPVT LVAYERVATG
SVVTVAGVSN FELIPNPELA KNLVTEYGRF DPGAMNYTKL ILSERDRLGI KTVWPTREYT
DFREYFMEVA DLNSPLKIAG AFGFKDIIRA IRRIAVPVVS TLFPPAAPLA HAIGEGVDYL
LGDEAQAASG TARAASGKAR AASGRIRQLT LAADKGYEVV ANLFQVPQNP VVDGILASPG
VLRGAHNLDC VLREGATLFP VVITTVEDAM TPKALNSKMF AVIEGVREDL QPPSQRGSFI
RTLSGHRVYG YAPDGVLPLE TGRDYTVVPI DDVWDDSIML SKDPIPPIVG NSGNLAIAYM
DVFRPKVPIH VAMTGALNAC GEIEKVSFRS TKLATAHRLG LKLAGPGAFD VNTGPNWATF
IKRFPHNPRD WDRLPYLNLP YLPPNAGRQY HLAMAASEFK ETPELESAVR AMEAAANVDP
LFQSALSVFM WLEENGIVTD MANFALSDPN AHRMRNFLAN APQAGSKSQR AKYGTAGYGV
EARGPTPEEA QREKDTRISK KMETMGIYFA TPEWVALNGH RGPSPGQLKY WQNTREIPDP
NEDYLDYVHA EKSRLASEEQ ILRAATSIYG APGQAEPPQA FIDEVAKVYE INHGRGPNQE
QMKDLLLTAM EMKHRNPRRA LPKPKPKPNA PTQRPPGRLG RWIRTVSDED LE


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