VP1_POVJC
ID VP1_POVJC Reviewed; 354 AA.
AC P03089;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Major capsid protein VP1;
DE AltName: Full=Major structural protein VP1;
OS JC polyomavirus (JCPyV) (JCV).
OC Viruses; Monodnaviria; Shotokuvirae; Cossaviricota; Papovaviricetes;
OC Sepolyvirales; Polyomaviridae; Betapolyomavirus.
OX NCBI_TaxID=10632;
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MAD-1;
RX PubMed=6086957; DOI=10.1128/jvi.51.2.458-469.1984;
RA Frisque R.J., Bream G.L., Cannella M.T.;
RT "Human polyomavirus JC virus genome.";
RL J. Virol. 51:458-469(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=C1, CY, G2, G3, HER1-BR, MAD11-BR, MAD8-BR, MY, N1, N4, NY-1B, and
RC Tokyo-1;
RX PubMed=8389465; DOI=10.1073/pnas.90.11.5062;
RA Iida T., Kitamura T., Guo J., Taguchi F., Aso Y., Nagashima K., Yogo Y.;
RT "Origin of JC polyomavirus variants associated with progressive multifocal
RT leukoencephalopathy.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:5062-5065(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=NY-1B;
RX PubMed=7915447; DOI=10.1007/bf01703608;
RA Yogo Y., Guo J., Iida T., Satoh K.I., Taguchi F., Takahashi H., Hall W.W.,
RA Nagashima K.;
RT "Occurrence of multiple JC virus variants with distinctive regulatory
RT sequences in the brain of a single patient with progressive multifocal
RT leukoencephalopathy.";
RL Virus Genes 8:99-105(1994).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=AIC-1A, TKY-2A, and YI;
RX PubMed=7823412; DOI=10.7883/yoken1952.47.167;
RA Kato K., Guo J., Taguchi F., Daimaru O., Tajima T., Haibara H., Matsuda J.,
RA Sumiya S., Yogo Y.;
RT "Phylogenetic comparison between archetypal and disease-associated JC virus
RT isolates in Japan.";
RL Jpn. J. Med. Sci. Biol. 47:167-178(1994).
RN [5]
RP FUNCTION.
RX PubMed=9573227; DOI=10.1128/jvi.72.6.4643-4649.1998;
RA Liu C.K., Wei G., Atwood W.J.;
RT "Infection of glial cells by the human polyomavirus JC is mediated by an N-
RT linked glycoprotein containing terminal alpha(2-6)-linked sialic acids.";
RL J. Virol. 72:4643-4649(1998).
RN [6]
RP FUNCTION.
RX PubMed=10666259; DOI=10.1128/jvi.74.5.2288-2292.2000;
RA Pho M.T., Ashok A., Atwood W.J.;
RT "JC virus enters human glial cells by clathrin-dependent receptor-mediated
RT endocytosis.";
RL J. Virol. 74:2288-2292(2000).
RN [7]
RP NUCLEAR LOCALIZATION SIGNAL.
RX PubMed=15069063; DOI=10.1074/jbc.m310827200;
RA Qu Q., Sawa H., Suzuki T., Semba S., Henmi C., Okada Y., Tsuda M.,
RA Tanaka S., Atwood W.J., Nagashima K.;
RT "Nuclear entry mechanism of the human polyomavirus JC virus-like particle:
RT role of importins and the nuclear pore complex.";
RL J. Biol. Chem. 279:27735-27742(2004).
RN [8]
RP INTERACTION WITH HOST 5HT2AR.
RX PubMed=15550673; DOI=10.1126/science.1103492;
RA Elphick G.F., Querbes W., Jordan J.A., Gee G.V., Eash S., Manley K.,
RA Dugan A., Stanifer M., Bhatnagar A., Kroeze W.K., Roth B.L., Atwood W.J.;
RT "The human polyomavirus, JCV, uses serotonin receptors to infect cells.";
RL Science 306:1380-1383(2004).
RN [9]
RP REVIEW.
RX PubMed=19157477; DOI=10.1016/j.virol.2008.12.022;
RA Sapp M., Day P.M.;
RT "Structure, attachment and entry of polyoma- and papillomaviruses.";
RL Virology 384:400-409(2009).
RN [10]
RP SUBCELLULAR LOCATION.
RX PubMed=15331723; DOI=10.1128/jvi.78.18.9890-9903.2004;
RA Shishido-Hara Y., Ichinose S., Higuchi K., Hara Y., Yasui K.;
RT "Major and minor capsid proteins of human polyomavirus JC cooperatively
RT accumulate to nuclear domain 10 for assembly into virions.";
RL J. Virol. 78:9890-9903(2004).
RN [11]
RP REVIEW.
RX PubMed=19157478; DOI=10.1016/j.virol.2008.12.021;
RA Neu U., Stehle T., Atwood W.J.;
RT "The Polyomaviridae: Contributions of virus structure to our understanding
RT of virus receptors and infectious entry.";
RL Virology 384:389-399(2009).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 23-290 IN COMPLEX WITH LINEAR
RP SIALYLATED PENTASACCHARIDE.
RX PubMed=20951965; DOI=10.1016/j.chom.2010.09.004;
RA Neu U., Maginnis M.S., Palma A.S., Stroeh L.J., Nelson C.D., Feizi T.,
RA Atwood W.J., Stehle T.;
RT "Structure-function analysis of the human JC polyomavirus establishes the
RT LSTc pentasaccharide as a functional receptor motif.";
RL Cell Host Microbe 8:309-319(2010).
CC -!- FUNCTION: Forms an icosahedral capsid with a T=7 symmetry and a 40 nm
CC diameter. The capsid is composed of 72 pentamers linked to each other
CC by disulfide bonds and associated with VP2 or VP3 proteins. Interacts
CC with a N-linked glycoprotein containing terminal alpha(2-6)-linked
CC sialic acids on the cell surface to provide virion attachment to target
CC cell. The serotonergic receptor 5HT2AR also acts as a cellular receptor
CC for JCV on human glial cells. Once attached, the virions enter
CC predominantly by a ligand-inducible clathrin-dependent pathway and
CC traffic to the ER. Inside the endoplasmic reticulum, the protein
CC folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby
CC triggering initial uncoating. Next, the virion uses the endoplasmic
CC reticulum-associated degradation machinery to probably translocate in
CC the cytosol before reaching the nucleus. Nuclear entry of the viral DNA
CC involves the selective exposure and importin recognition of VP2/Vp3
CC nuclear localization signal. In late phase of infection, neo-
CC synthesized VP1 encapsulates replicated genomic DNA at nuclear domains
CC called promyelocytic leukemia (PML) bodies, and participates in
CC rearranging nucleosomes around the viral DNA.
CC {ECO:0000269|PubMed:10666259, ECO:0000269|PubMed:9573227,
CC ECO:0000305|PubMed:19157478}.
CC -!- SUBUNIT: Homomultimer; disulfide-linked. The virus capsid is composed
CC of 72 icosahedral units, each one composed of five disulfide-linked
CC copies of VP1. Interacts with minor capsid proteins VP2 and VP3 (By
CC similarity). Interacts with host 5HT2AR. {ECO:0000250,
CC ECO:0000269|PubMed:15550673, ECO:0000269|PubMed:20951965}.
CC -!- SUBCELLULAR LOCATION: Virion. Host nucleus
CC {ECO:0000269|PubMed:15331723}. Note=Virions are efficiently assembled
CC at nuclear domain 10 (ND10), which is also known as promyelocytic
CC leukemia (PML) nuclear bodies. {ECO:0000269|PubMed:15331723}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing, Alternative initiation; Named isoforms=5;
CC Name=VP1; Synonyms=Major capsid protein VP1;
CC IsoId=P03089-1; Sequence=Displayed;
CC Name=VP2; Synonyms=Minor capsid protein VP2;
CC IsoId=P03095-1; Sequence=External;
CC Name=VP3; Synonyms=Minor capsid protein VP3;
CC IsoId=P03095-2; Sequence=External;
CC Name=VP4; Synonyms=Viroporin VP4;
CC IsoId=P03095-3; Sequence=External;
CC Name=Agno;
CC IsoId=P03086-1; Sequence=External;
CC -!- DOMAIN: The intrinsically disordered C-terminal arm interacts with
CC neighboring pentamers. The unstructured nature of this region allows to
CC make different interactions depending on the structural context:
CC pentamers present at the 12 icosahedral fivefold axes bind five
CC pentamers, whereas pentamers present at the 60 icosahedral six-fold
CC axes interact with six pentamers. {ECO:0000250|UniProtKB:P03087}.
CC -!- MISCELLANEOUS: [Isoform VP1]: Produced by alternative splicing of the
CC late mRNA.
CC -!- SIMILARITY: Belongs to the polyomaviruses coat protein VP1 family.
CC {ECO:0000305}.
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DR EMBL; J02226; AAA82101.1; -; Genomic_DNA.
DR EMBL; D11356; BAA01958.1; -; Genomic_DNA.
DR EMBL; D11357; BAA01959.1; -; Genomic_DNA.
DR EMBL; D11358; BAA01960.1; -; Genomic_DNA.
DR EMBL; D11359; BAA01961.1; -; Genomic_DNA.
DR EMBL; D11360; BAA01962.1; -; Genomic_DNA.
DR EMBL; D11361; BAA01963.1; -; Genomic_DNA.
DR EMBL; D11362; BAA01964.1; -; Genomic_DNA.
DR EMBL; D11363; BAA01965.1; -; Genomic_DNA.
DR EMBL; D11364; BAA01966.1; -; Genomic_DNA.
DR EMBL; D11365; BAA01967.1; -; Genomic_DNA.
DR EMBL; D11366; BAA01968.1; -; Genomic_DNA.
DR EMBL; D11368; BAA01970.1; -; Genomic_DNA.
DR EMBL; D26589; BAA05636.1; -; Genomic_DNA.
DR EMBL; D26591; BAA05638.1; -; Genomic_DNA.
DR EMBL; D26592; BAA05639.1; -; Genomic_DNA.
DR PIR; A03626; VVVP1J.
DR RefSeq; NP_043511.1; NC_001699.1. [P03089-1]
DR PDB; 3NXD; X-ray; 2.00 A; A/B/C/D/E=23-290.
DR PDB; 3NXG; X-ray; 1.95 A; A/B/C/D/E=23-290.
DR PDB; 4JCD; X-ray; 2.00 A; A/B/C/D/E=23-290.
DR PDB; 4JCE; X-ray; 1.90 A; A/B/C/D/E=23-290.
DR PDB; 4JCF; X-ray; 2.20 A; A/B/C/D/E=23-290.
DR PDB; 4WDY; X-ray; 1.90 A; A/B/C/D/E=23-290.
DR PDB; 4WDZ; X-ray; 1.80 A; A/B/C/D/E=23-290.
DR PDB; 4WE0; X-ray; 2.10 A; A/B/C/D/E=23-290.
DR PDB; 4X14; X-ray; 2.30 A; A/B/C/D/E=23-290.
DR PDB; 4X15; X-ray; 2.11 A; A/B/C/D/E=23-290.
DR PDB; 4X16; X-ray; 1.80 A; A/B/C/D/E=23-290.
DR PDB; 4X17; X-ray; 1.75 A; A/B/C/D/E=23-290.
DR PDBsum; 3NXD; -.
DR PDBsum; 3NXG; -.
DR PDBsum; 4JCD; -.
DR PDBsum; 4JCE; -.
DR PDBsum; 4JCF; -.
DR PDBsum; 4WDY; -.
DR PDBsum; 4WDZ; -.
DR PDBsum; 4WE0; -.
DR PDBsum; 4X14; -.
DR PDBsum; 4X15; -.
DR PDBsum; 4X16; -.
DR PDBsum; 4X17; -.
DR SMR; P03089; -.
DR UniLectin; P03089; -.
DR PRIDE; P03089; -.
DR DNASU; 1489518; -.
DR GeneID; 1489518; -.
DR KEGG; vg:1489518; -.
DR EvolutionaryTrace; P03089; -.
DR Proteomes; UP000008478; Genome.
DR GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0039620; C:T=7 icosahedral viral capsid; IEA:UniProtKB-KW.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR GO; GO:0075512; P:clathrin-dependent endocytosis of virus by host cell; IEA:UniProtKB-KW.
DR GO; GO:0019062; P:virion attachment to host cell; IEA:UniProtKB-KW.
DR Gene3D; 2.60.175.10; -; 1.
DR InterPro; IPR000662; Capsid_VP1_Polyomavir.
DR InterPro; IPR011222; dsDNA_vir_gr_I_capsid.
DR InterPro; IPR036931; Polyomavir_VP1_sf.
DR Pfam; PF00718; Polyoma_coat; 1.
DR PIRSF; PIRSF003376; Capsid_VP1_Polyomavir; 1.
DR SUPFAM; SSF88648; SSF88648; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative initiation; Alternative splicing; Capsid protein;
KW Clathrin-mediated endocytosis of virus by host; Disulfide bond;
KW Host nucleus; Host-virus interaction; Late protein; Phosphoprotein;
KW T=7 icosahedral capsid protein; Viral attachment to host cell;
KW Viral penetration into host cytoplasm; Virion; Virus endocytosis by host;
KW Virus entry into host cell.
FT CHAIN 1..354
FT /note="Major capsid protein VP1"
FT /id="PRO_0000115021"
FT REGION 294..354
FT /note="C-terminal arm"
FT /evidence="ECO:0000250|UniProtKB:P03087"
FT MOD_RES 330
FT /note="Phosphothreonine; by host"
FT /evidence="ECO:0000250"
FT DISULFID 97
FT /note="Interchain (with C-97)"
FT /evidence="ECO:0000250"
FT VARIANT 66
FT /note="D -> H (in strain: Isolate MAD11-BR)"
FT VARIANT 74
FT /note="N -> S (in strain: Isolate NY-1B, Isolate N1 and
FT Isolate G3)"
FT VARIANT 75
FT /note="R -> K (in strain: Isolate YI, Isolate TKY-2A,
FT Isolate MAD8-BR, Isolate HER1-BR, Isolate NY-1B, Isolate
FT N1, Isolate N4, Isolate G3, Isolate C1, Isolate CY, Isolate
FT MY, Isolate AIC-1A and Isolate Tokyo-1)"
FT VARIANT 113
FT /note="I -> L (in strain: Isolate YI, Isolate C1, Isolate
FT AIC-1A and Isolate Tokyo-1)"
FT VARIANT 117
FT /note="S -> T (in strain: Isolate YI, Isolate TKY-2A,
FT Isolate MAD8-BR, Isolate N4, Isolate C1, Isolate CY,
FT Isolate MY, Isolate AIC-1A and Isolate Tokyo-1)"
FT VARIANT 128
FT /note="T -> A (in strain: Isolate MAD8-BR, Isolate NY-1B,
FT Isolate N1, Isolate G3 and Isolate N4)"
FT VARIANT 158
FT /note="L -> V (in strain: Isolate YI, Isolate TKY-2A,
FT Isolate MAD8-BR, Isolate NY-1B, Isolate N1, Isolate N4,
FT Isolate G3, Isolate C1, Isolate CY, Isolate MY, Isolate
FT AIC-1A and Isolate Tokyo-1)"
FT VARIANT 267
FT /note="S -> L (in strain: Isolate HER1-BR)"
FT VARIANT 269
FT /note="S -> F (in strain: Isolate MAD8-BR)"
FT VARIANT 269
FT /note="S -> T (in strain: Isolate YI)"
FT VARIANT 269
FT /note="S -> Y (in strain: Isolate TKY-2A)"
FT VARIANT 321
FT /note="V -> I (in strain: Isolate C1)"
FT VARIANT 345
FT /note="K -> R (in strain: Isolate YI, Isolate TKY-2A,
FT Isolate MAD8-BR, Isolate N1, Isolate N4, Isolate G4,
FT Isolate C1, Isolate CY, Isolate MY, Isolate AIC-1A and
FT Isolate Tokyo-1)"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:4X17"
FT HELIX 34..36
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 37..44
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 65..68
FT /evidence="ECO:0007829|PDB:4X17"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 82..87
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 101..113
FT /evidence="ECO:0007829|PDB:4X17"
FT HELIX 115..119
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 122..125
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 141..150
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 153..156
FT /evidence="ECO:0007829|PDB:4X17"
FT HELIX 177..180
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:4X17"
FT TURN 193..195
FT /evidence="ECO:0007829|PDB:4JCE"
FT HELIX 198..200
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 211..218
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 226..232
FT /evidence="ECO:0007829|PDB:4X17"
FT HELIX 248..250
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 251..265
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 270..274
FT /evidence="ECO:0007829|PDB:4X17"
FT STRAND 276..288
FT /evidence="ECO:0007829|PDB:4X17"
SQ SEQUENCE 354 AA; 39609 MW; 33CDA3DD93026ED0 CRC64;
MAPTKRKGER KDPVQVPKLL IRGGVEVLEV KTGVDSITEV ECFLTPEMGD PDEHLRGFSK
SISISDTFES DSPNRDMLPC YSVARIPLPN LNEDLTCGNI LMWEAVTLKT EVIGVTSLMN
VHSNGQATHD NGAGKPVQGT SFHFFSVGGE ALELQGVLFN YRTKYPDGTI FPKNATVQSQ
VMNTEHKAYL DKNKAYPVEC WVPDPTRNEN TRYFGTLTGG ENVPPVLHIT NTATTVLLDE
FGVGPLCKGD NLYLSAVDVC GMFTNRSGSQ QWRGLSRYFK VQLRKRRVKN PYPISFLLTD
LINRRTPRVD GQPMYGMDAQ VEEVRVFEGT EELPGDPDMM RYVDKYGQLQ TKML
