POLS_IBDVC
ID POLS_IBDVC Reviewed; 1012 AA.
AC P15480;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1990, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Structural polyprotein;
DE Short=PP;
DE Contains:
DE RecName: Full=Precursor of VP2;
DE Short=Pre-VP2;
DE Contains:
DE RecName: Full=Capsid protein VP2;
DE Contains:
DE RecName: Full=Structural peptide 1;
DE Short=p1;
DE AltName: Full=pep46;
DE Contains:
DE RecName: Full=Structural peptide 2;
DE Short=p2;
DE AltName: Full=pep7a;
DE Contains:
DE RecName: Full=Structural peptide 3;
DE Short=p3;
DE AltName: Full=pep7b;
DE Contains:
DE RecName: Full=Structural peptide 4;
DE Short=p4;
DE AltName: Full=pep11;
DE Contains:
DE RecName: Full=Protease VP4;
DE EC=3.4.21.-;
DE AltName: Full=Non-structural protein VP4;
DE Short=NS;
DE Contains:
DE RecName: Full=Capsid protein VP3;
OS Avian infectious bursal disease virus (strain Cu-1) (IBDV) (Gumboro disease
OS virus).
OC Viruses; Riboviria; Orthornavirae; Birnaviridae; Avibirnavirus.
OX NCBI_TaxID=10998;
OH NCBI_TaxID=9031; Gallus gallus (Chicken).
OH NCBI_TaxID=9103; Meleagris gallopavo (Wild turkey).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=2552417; DOI=10.1093/nar/17.19.7982;
RA Spies U., Mueller H., Becht H.;
RT "Nucleotide sequence of infectious bursal disease virus genome segment A
RT delineates two major open reading frames.";
RL Nucleic Acids Res. 17:7982-7982(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=2161902; DOI=10.1099/0022-1317-71-6-1303;
RA Bayliss C.D., Spies U., Shaw K., Peters R.W., Papageorgiou A., Mueller H.,
RA Boursnell M.E.G.;
RT "A comparison of the sequences of segment A of four infectious bursal
RT disease virus strains and identification of a variable region in VP2.";
RL J. Gen. Virol. 71:1303-1312(1990).
RN [3]
RP PROTEIN SEQUENCE OF 513-519 AND 756-762, ACTIVE SITES OF PROTEASE VP4,
RP PROTEOLYTIC PROCESSING OF POLYPROTEIN, AND MUTAGENESIS OF 487-ALA-ALA-488;
RP 495-ALA-ALA-494; 501-ALA-ALA-502; 512-ALA-ALA-513; SER-652; LYS-692 AND
RP 755-ALA-ALA-756.
RC STRAIN=Isolate vaccine CT;
RX PubMed=10725424; DOI=10.1099/0022-1317-81-4-983;
RA Lejal N., Da Costa B., Huet J.-C., Delmas B.;
RT "Role of Ser-652 and Lys-692 in the protease activity of infectious bursal
RT disease virus VP4 and identification of its substrate cleavage sites.";
RL J. Gen. Virol. 81:983-992(2000).
RN [4]
RP PROTEIN SEQUENCE OF 442-456 AND 488-512, PROTEOLYTIC PROCESSING OF
RP POLYPROTEIN, AND MUTAGENESIS OF ALA-441; PHE-442; 487-ALA-ALA-488;
RP 494-ALA-ALA-495; 501-ALA-ALA-502; ALA-512 AND ALA-513.
RC STRAIN=Isolate vaccine CT;
RX PubMed=11836417; DOI=10.1128/jvi.76.5.2393-2402.2002;
RA Da Costa B., Chevalier C., Henry C., Huet J.-C., Petit S., Lepault J.,
RA Boot H., Delmas B.;
RT "The capsid of infectious bursal disease virus contains several small
RT peptides arising from the maturation process of pVP2.";
RL J. Virol. 76:2393-2402(2002).
RN [5]
RP 3D-STRUCTURE MODELING, AND STRUCTURE BY ELECTRON MICROSCOPY (15 ANGSTROMS)
RP OF VIRAL PARTICLES.
RC STRAIN=Isolate vaccine CT;
RX PubMed=16033982; DOI=10.1099/vir.0.80942-0;
RA Pous J., Chevalier C., Ouldali M., Navaza J., Delmas B., Lepault J.;
RT "Structure of birnavirus-like particles determined by combined electron
RT cryomicroscopy and X-ray crystallography.";
RL J. Gen. Virol. 86:2339-2346(2005).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 1-441.
RX PubMed=15797378; DOI=10.1016/j.cell.2005.01.009;
RA Coulibaly F., Chevalier C., Gutsche I., Pous J., Navaza J., Bressanelli S.,
RA Delmas B., Rey F.A.;
RT "The birnavirus crystal structure reveals structural relationships among
RT icosahedral viruses.";
RL Cell 120:761-772(2005).
CC -!- FUNCTION: Capsid protein VP2 self assembles to form an icosahedral
CC capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of
CC 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also
CC involved in attachment and entry into the host cell by interacting with
CC host ITGA4/ITGB1 (By similarity). {ECO:0000250}.
CC -!- FUNCTION: The precursor of VP2 plays an important role in capsid
CC assembly. First, pre-VP2 and VP2 oligomers assemble to form a
CC procapsid. Then, the pre-VP2 intermediates may be processed into VP2
CC proteins by proteolytic cleavage mediated by VP4 to obtain the mature
CC virion. The final capsid is composed of pentamers and hexamers but VP2
CC has a natural tendency to assemble into all-pentameric structures.
CC Therefore pre-VP2 may be required to allow formation of the hexameric
CC structures (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Protease VP4 is a serine protease that cleaves the
CC polyprotein into its final products. Pre-VP2 is first partially
CC cleaved, and may be completely processed by VP4 upon capsid maturation.
CC {ECO:0000255|PROSITE-ProRule:PRU00881}.
CC -!- FUNCTION: Capsid protein VP3 plays a key role in virion assembly by
CC providing a scaffold for the capsid made of VP2. May self-assemble to
CC form a T=4-like icosahedral inner-capsid composed of at least 180
CC trimers. Plays a role in genomic RNA packaging by recruiting VP1 into
CC the capsid and interacting with the dsRNA genome segments to form a
CC ribonucleoprotein complex. Additionally, the interaction of the VP3 C-
CC terminal tail with VP1 removes the inherent structural blockade of the
CC polymerase active site. Thus, VP3 can also function as a
CC transcriptional activator (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Structural peptide 1 is a small peptide derived from pre-VP2
CC C-terminus. It destabilizes and perforates cell membranes, suggesting a
CC role during entry (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Structural peptide 2 is a small peptide derived from pVP2 C-
CC terminus. It is not essential for the virus viability, but viral growth
CC is affected when missing.
CC -!- FUNCTION: Structural peptide 3 is a small peptide derived from pVP2 C-
CC terminus. It is not essential for the virus viability, but viral growth
CC is affected when missing.
CC -!- FUNCTION: Structural peptide 4 is a small peptide derived from pVP2 C-
CC terminus. It is essential for the virus viability.
CC -!- SUBUNIT: Capsid protein VP2 is a homotrimer. A central divalent metal
CC stabilizes the VP2 trimer, possibly calcium (By similarity). Capsid
CC protein VP3 is a homodimer. Capsid protein VP2 interacts with host
CC ITGA4/ITGB1. Capsid protein VP3 interacts (via C-terminus) with VP1 in
CC the cytoplasm. Capsid VP3 interacts with VP2 (By similarity).
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: [Capsid protein VP2]: Virion {ECO:0000305}. Host
CC cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Capsid protein VP3]: Virion {ECO:0000305}. Host
CC cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Structural peptide 1]: Virion {ECO:0000305}.
CC Host cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Structural peptide 2]: Virion {ECO:0000305}.
CC Host cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Structural peptide 3]: Virion {ECO:0000305}.
CC Host cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Structural peptide 4]: Virion {ECO:0000305}.
CC Host cytoplasm {ECO:0000305}.
CC -!- PTM: Specific enzymatic cleavages yield mature proteins. The capsid
CC assembly seems to be regulated by polyprotein processing. The protease
CC VP4 cleaves itself off the polyprotein, thus releasing pre-VP2 and VP3
CC within the infected cell. During capsid assembly, the C-terminus of
CC pre-VP2 is further processed by VP4, giving rise to VP2, the external
CC capsid protein and three small peptides that all stay closely
CC associated with the capsid (By similarity). {ECO:0000250}.
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DR EMBL; X16107; CAA34234.1; -; Genomic_RNA.
DR EMBL; D00867; BAA00740.1; -; Genomic_RNA.
DR PIR; A35353; GNXSCU.
DR PDB; 1WCD; X-ray; 3.00 A; J=1-441.
DR PDB; 1WCE; X-ray; 7.00 A; A/B/C/D/E/F/G/H/I/J/K/L/M=1-441.
DR PDBsum; 1WCD; -.
DR PDBsum; 1WCE; -.
DR BMRB; P15480; -.
DR SMR; P15480; -.
DR MEROPS; S50.002; -.
DR EvolutionaryTrace; P15480; -.
DR GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0039621; C:T=13 icosahedral viral capsid; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008236; F:serine-type peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR Gene3D; 1.10.150.620; -; 1.
DR Gene3D; 1.10.8.880; -; 1.
DR Gene3D; 2.60.120.20; -; 1.
DR InterPro; IPR002662; Birna_VP2.
DR InterPro; IPR002663; Birna_VP3.
DR InterPro; IPR043048; Birna_VP3_dom1.
DR InterPro; IPR043049; Birna_VP3_dom2.
DR InterPro; IPR025775; Birna_VP4_Prtase_dom.
DR InterPro; IPR029053; Viral_coat.
DR Pfam; PF01766; Birna_VP2; 1.
DR Pfam; PF01767; Birna_VP3; 1.
DR Pfam; PF01768; Birna_VP4; 1.
DR PROSITE; PS51548; BIRNAVIRUS_VP4_PRO; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Capsid protein; Direct protein sequencing; Host cytoplasm;
KW Hydrolase; Metal-binding; Protease; Serine protease;
KW T=13 icosahedral capsid protein; Virion.
FT CHAIN 1..1012
FT /note="Structural polyprotein"
FT /id="PRO_0000392588"
FT CHAIN 1..512
FT /note="Precursor of VP2"
FT /id="PRO_0000392589"
FT CHAIN 1..441
FT /note="Capsid protein VP2"
FT /id="PRO_0000036765"
FT PEPTIDE 442..487
FT /note="Structural peptide 1"
FT /evidence="ECO:0000269|PubMed:11836417"
FT /id="PRO_0000227831"
FT PEPTIDE 488..494
FT /note="Structural peptide 2"
FT /id="PRO_0000227832"
FT PEPTIDE 495..501
FT /note="Structural peptide 3"
FT /id="PRO_0000227833"
FT PEPTIDE 502..512
FT /note="Structural peptide 4"
FT /evidence="ECO:0000269|PubMed:10725424"
FT /id="PRO_0000227834"
FT CHAIN 513..755
FT /note="Protease VP4"
FT /id="PRO_0000036766"
FT CHAIN 756..1012
FT /note="Capsid protein VP3"
FT /id="PRO_0000036767"
FT DOMAIN 513..755
FT /note="Peptidase S50"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00881"
FT REGION 969..1012
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1003..1012
FT /note="Interaction with VP1 protein"
FT /evidence="ECO:0000250"
FT ACT_SITE 652
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00881,
FT ECO:0000269|PubMed:10725424"
FT ACT_SITE 692
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00881,
FT ECO:0000269|PubMed:10725424"
FT BINDING 30
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="ligand shared between trimeric partners"
FT /evidence="ECO:0000250"
FT SITE 441..442
FT /note="Cleavage; by protease VP4"
FT SITE 487..488
FT /note="Cleavage; by protease VP4"
FT SITE 494..495
FT /note="Cleavage; by protease VP4"
FT SITE 501..502
FT /note="Cleavage; by protease VP4"
FT SITE 512..513
FT /note="Cleavage; by protease VP4"
FT SITE 755..756
FT /note="Cleavage; by protease VP4"
FT MUTAGEN 441
FT /note="A->E,Q,R: Lethal for the virus."
FT /evidence="ECO:0000269|PubMed:11836417"
FT MUTAGEN 442
FT /note="F->D,G,N: Lethal for the virus."
FT /evidence="ECO:0000269|PubMed:11836417"
FT MUTAGEN 487..488
FT /note="AA->EF: No effect on virus growth."
FT /evidence="ECO:0000269|PubMed:10725424,
FT ECO:0000269|PubMed:11836417"
FT MUTAGEN 487..488
FT /note="AA->QL: No effect on polyprotein processing."
FT /evidence="ECO:0000269|PubMed:10725424,
FT ECO:0000269|PubMed:11836417"
FT MUTAGEN 494..495
FT /note="AA->EF: 80% reduction of virus growth, small-plaque
FT phenotype."
FT /evidence="ECO:0000269|PubMed:10725424,
FT ECO:0000269|PubMed:11836417"
FT MUTAGEN 494..495
FT /note="AA->QL: No effect on polyprotein processing."
FT /evidence="ECO:0000269|PubMed:10725424,
FT ECO:0000269|PubMed:11836417"
FT MUTAGEN 501..502
FT /note="AA->EF: No effect on virus growth."
FT /evidence="ECO:0000269|PubMed:10725424,
FT ECO:0000269|PubMed:11836417"
FT MUTAGEN 501..502
FT /note="AA->QL: No effect on polyprotein processing."
FT /evidence="ECO:0000269|PubMed:10725424,
FT ECO:0000269|PubMed:11836417"
FT MUTAGEN 512..513
FT /note="AA->EF: Gives rise to uncleaved pVP2-VP4 and two
FT shorter forms of VP2. Lethal for the virus."
FT /evidence="ECO:0000269|PubMed:10725424"
FT MUTAGEN 512
FT /note="A->D,L,N,V: Lethal for the virus."
FT /evidence="ECO:0000269|PubMed:11836417"
FT MUTAGEN 512
FT /note="A->G: Smaller amounts of cleaved forms of pVP2. No
FT effect virus growth."
FT /evidence="ECO:0000269|PubMed:11836417"
FT MUTAGEN 512
FT /note="A->I,L,N,R,S,V: Lethal for the virus."
FT /evidence="ECO:0000269|PubMed:11836417"
FT MUTAGEN 513
FT /note="A->G: No effect on polyprotein processing and virus
FT growth."
FT /evidence="ECO:0000269|PubMed:11836417"
FT MUTAGEN 652
FT /note="S->A,T: Complete loss of polyprotein processing."
FT /evidence="ECO:0000269|PubMed:10725424"
FT MUTAGEN 652
FT /note="S->C: Partial loss of polyprotein processing."
FT /evidence="ECO:0000269|PubMed:10725424"
FT MUTAGEN 692
FT /note="K->A,R,H: Complete loss of polyprotein processing."
FT /evidence="ECO:0000269|PubMed:10725424"
FT MUTAGEN 755..756
FT /note="AA->EF: Gives rise to pVP2 and uncleaved VP3-VP4."
FT /evidence="ECO:0000269|PubMed:10725424"
FT HELIX 14..19
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 21..23
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 36..48
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 64..74
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 96..110
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 123..131
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:1WCD"
FT TURN 141..143
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 144..146
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 154..159
FT /evidence="ECO:0007829|PDB:1WCD"
FT TURN 160..162
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 204..218
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 225..238
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 240..249
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 251..265
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 270..282
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 284..286
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 288..293
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 298..300
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 305..314
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 325..337
FT /evidence="ECO:0007829|PDB:1WCD"
FT TURN 338..341
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 349..356
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 362..375
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 379..381
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 394..403
FT /evidence="ECO:0007829|PDB:1WCD"
FT TURN 404..409
FT /evidence="ECO:0007829|PDB:1WCD"
FT STRAND 412..415
FT /evidence="ECO:0007829|PDB:1WCD"
FT HELIX 416..422
FT /evidence="ECO:0007829|PDB:1WCD"
FT TURN 423..427
FT /evidence="ECO:0007829|PDB:1WCD"
SQ 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
