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Major capsid protein VP1 (Major structural protein VP1)

 VP1_POVJC               Reviewed;         354 AA.
P03089;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
21-JUL-1986, sequence version 1.
25-OCT-2017, entry version 103.
RecName: Full=Major capsid protein VP1;
AltName: Full=Major structural protein VP1;
JC polyomavirus (JCPyV) (JCV).
Viruses; dsDNA viruses, no RNA stage; Polyomaviridae.
NCBI_TaxID=10632;
NCBI_TaxID=9606; Homo sapiens (Human).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=MAD-1;
PubMed=6086957;
Frisque R.J., Bream G.L., Cannella M.T.;
"Human polyomavirus JC virus genome.";
J. Virol. 51:458-469(1984).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=C1, CY, G2, G3, HER1-BR, MAD11-BR, MAD8-BR, MY, N1, N4, NY-1B,
and Tokyo-1;
PubMed=8389465; DOI=10.1073/pnas.90.11.5062;
Iida T., Kitamura T., Guo J., Taguchi F., Aso Y., Nagashima K.,
Yogo Y.;
"Origin of JC polyomavirus variants associated with progressive
multifocal leukoencephalopathy.";
Proc. Natl. Acad. Sci. U.S.A. 90:5062-5065(1993).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=NY-1B;
PubMed=7915447; DOI=10.1007/BF01703608;
Yogo Y., Guo J., Iida T., Satoh K.I., Taguchi F., Takahashi H.,
Hall W.W., Nagashima K.;
"Occurrence of multiple JC virus variants with distinctive regulatory
sequences in the brain of a single patient with progressive multifocal
leukoencephalopathy.";
Virus Genes 8:99-105(1994).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=AIC-1A, TKY-2A, and YI;
PubMed=7823412;
Kato K., Guo J., Taguchi F., Daimaru O., Tajima T., Haibara H.,
Matsuda J., Sumiya S., Yogo Y.;
"Phylogenetic comparison between archetypal and disease-associated JC
virus isolates in Japan.";
Jpn. J. Med. Sci. Biol. 47:167-178(1994).
[5]
VIRION ENTRY.
PubMed=9573227;
Liu C.K., Wei G., Atwood W.J.;
"Infection of glial cells by the human polyomavirus JC is mediated by
an N-linked glycoprotein containing terminal alpha(2-6)-linked sialic
acids.";
J. Virol. 72:4643-4649(1998).
[6]
FUNCTION.
PubMed=10666259; DOI=10.1128/JVI.74.5.2288-2292.2000;
Pho M.T., Ashok A., Atwood W.J.;
"JC virus enters human glial cells by clathrin-dependent receptor-
mediated endocytosis.";
J. Virol. 74:2288-2292(2000).
[7]
NUCLEAR SIGNAL.
PubMed=15069063; DOI=10.1074/jbc.M310827200;
Qu Q., Sawa H., Suzuki T., Semba S., Henmi C., Okada Y., Tsuda M.,
Tanaka S., Atwood W.J., Nagashima K.;
"Nuclear entry mechanism of the human polyomavirus JC virus-like
particle: role of importins and the nuclear pore complex.";
J. Biol. Chem. 279:27735-27742(2004).
[8]
INTERACTION WITH HOST 5HT2AR.
PubMed=15550673; DOI=10.1126/science.1103492;
Elphick G.F., Querbes W., Jordan J.A., Gee G.V., Eash S., Manley K.,
Dugan A., Stanifer M., Bhatnagar A., Kroeze W.K., Roth B.L.,
Atwood W.J.;
"The human polyomavirus, JCV, uses serotonin receptors to infect
cells.";
Science 306:1380-1383(2004).
[9]
REVIEW.
PubMed=19157477; DOI=10.1016/j.virol.2008.12.022;
Sapp M., Day P.M.;
"Structure, attachment and entry of polyoma- and papillomaviruses.";
Virology 384:400-409(2009).
[10]
ASSEMBLY AT PML NUCLEAR BODIES.
PubMed=15331723; DOI=10.1128/JVI.78.18.9890-9903.2004;
Shishido-Hara Y., Ichinose S., Higuchi K., Hara Y., Yasui K.;
"Major and minor capsid proteins of human polyomavirus JC
cooperatively accumulate to nuclear domain 10 for assembly into
virions.";
J. Virol. 78:9890-9903(2004).
[11]
REVIEW.
PubMed=19157478; DOI=10.1016/j.virol.2008.12.021;
Neu U., Stehle T., Atwood W.J.;
"The Polyomaviridae: Contributions of virus structure to our
understanding of virus receptors and infectious entry.";
Virology 384:389-399(2009).
[12]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 23-290 IN COMPLEX WITH LINEAR
SIALYLATED PENTASACCHARIDE.
PubMed=20951965; DOI=10.1016/j.chom.2010.09.004;
Neu U., Maginnis M.S., Palma A.S., Stroeh L.J., Nelson C.D., Feizi T.,
Atwood W.J., Stehle T.;
"Structure-function analysis of the human JC polyomavirus establishes
the LSTc pentasaccharide as a functional receptor motif.";
Cell Host Microbe 8:309-319(2010).
-!- FUNCTION: Forms an icosahedral capsid with a T=7 symmetry and a 40
nm diameter. The capsid is composed of 72 pentamers linked to each
other by disulfide bonds and associated with VP2 or VP3 proteins.
Interacts with a N-linked glycoprotein containing terminal
alpha(2-6)-linked sialic acids on the cell surface to provide
virion attachment to target cell. The serotonergic receptor 5HT2AR
also acts as a cellular receptor for JCV on human glial cells.
Once attached, the virions enter predominantly by a ligand-
inducible clathrin-dependent pathway and traffic to the ER. Inside
the endoplasmic reticulum, the protein folding machinery
isomerizes VP1 interpentamer disulfide bonds, thereby triggering
initial uncoating. Next, the virion uses the endoplasmic
reticulum-associated degradation machinery to probably translocate
in the cytosol before reaching the nucleus. Nuclear entry of the
viral DNA involves the selective exposure and importin recognition
of VP2/Vp3 nuclear localization signal. In late phase of
infection, neo-synthesized VP1 encapsulates replicated genomic DNA
at nuclear domains called promyelocytic leukemia (PML) bodies, and
participates in rearranging nucleosomes around the viral DNA.
{ECO:0000269|PubMed:10666259}.
-!- SUBUNIT: Homomultimer; disulfide-linked. The virus capsid is
composed of 72 icosahedral units, each one composed of five
disulfide-linked copies of VP1. Interacts with minor capsid
proteins VP2 and VP3 (By similarity). Interacts with host 5HT2AR.
{ECO:0000250, ECO:0000269|PubMed:15550673,
ECO:0000269|PubMed:20951965}.
-!- SUBCELLULAR LOCATION: Virion. Host nucleus {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing, Alternative initiation; Named isoforms=5;
Name=VP1; Synonyms=Major capsid protein VP1;
IsoId=P03089-1; Sequence=Displayed;
Note=Produced by alternative splicing of the late mRNA.;
Name=VP2; Synonyms=Minor capsid protein VP2;
IsoId=P03095-1; Sequence=External;
Note=Produced by alternative splicing of the late mRNA.;
Name=VP3; Synonyms=Minor capsid protein VP3;
IsoId=P03095-2; Sequence=External;
Note=Produced by alternative initiation at Met-120 of isoform
VP2.;
Name=VP4; Synonyms=Viroporin VP4;
IsoId=P03095-3; Sequence=External;
Note=Produced by alternative initiation at Met-229 of isoform
VP2.;
Name=Agno;
IsoId=P03086-1; Sequence=External;
Note=Produced by alternative initiation of the late mRNA.;
-!- DOMAIN: The intrinsically disordered C-terminal region interacts
with neighboring pentamers. The unstructured nature of this region
allows to make different interactions depending on the structural
context: pentamers present at the 12 icosahedral fivefold axes
bind five pentamers, when pentamers present at the 60 icosahedral
six-fold axes interacts with six pentamers (By similarity).
{ECO:0000250}.
-!- SIMILARITY: Belongs to the polyomaviruses coat protein VP1 family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; J02226; AAA82101.1; -; Genomic_DNA.
EMBL; D11356; BAA01958.1; -; Genomic_DNA.
EMBL; D11357; BAA01959.1; -; Genomic_DNA.
EMBL; D11358; BAA01960.1; -; Genomic_DNA.
EMBL; D11359; BAA01961.1; -; Genomic_DNA.
EMBL; D11360; BAA01962.1; -; Genomic_DNA.
EMBL; D11361; BAA01963.1; -; Genomic_DNA.
EMBL; D11362; BAA01964.1; -; Genomic_DNA.
EMBL; D11363; BAA01965.1; -; Genomic_DNA.
EMBL; D11364; BAA01966.1; -; Genomic_DNA.
EMBL; D11365; BAA01967.1; -; Genomic_DNA.
EMBL; D11366; BAA01968.1; -; Genomic_DNA.
EMBL; D11368; BAA01970.1; -; Genomic_DNA.
EMBL; D26589; BAA05636.1; -; Genomic_DNA.
EMBL; D26591; BAA05638.1; -; Genomic_DNA.
EMBL; D26592; BAA05639.1; -; Genomic_DNA.
PIR; A03626; VVVP1J.
RefSeq; NP_043511.1; NC_001699.1. [P03089-1]
PDB; 3NXD; X-ray; 2.00 A; A/B/C/D/E=23-290.
PDB; 3NXG; X-ray; 1.95 A; A/B/C/D/E=23-290.
PDB; 4JCD; X-ray; 2.00 A; A/B/C/D/E=23-290.
PDB; 4JCE; X-ray; 1.90 A; A/B/C/D/E=23-290.
PDB; 4JCF; X-ray; 2.20 A; A/B/C/D/E=23-290.
PDB; 4WDY; X-ray; 1.90 A; A/B/C/D/E=23-290.
PDB; 4WDZ; X-ray; 1.80 A; A/B/C/D/E=23-290.
PDB; 4WE0; X-ray; 2.10 A; A/B/C/D/E=23-290.
PDB; 4X14; X-ray; 2.30 A; A/B/C/D/E=23-290.
PDB; 4X15; X-ray; 2.11 A; A/B/C/D/E=23-290.
PDB; 4X16; X-ray; 1.80 A; A/B/C/D/E=23-290.
PDB; 4X17; X-ray; 1.75 A; A/B/C/D/E=23-290.
PDBsum; 3NXD; -.
PDBsum; 3NXG; -.
PDBsum; 4JCD; -.
PDBsum; 4JCE; -.
PDBsum; 4JCF; -.
PDBsum; 4WDY; -.
PDBsum; 4WDZ; -.
PDBsum; 4WE0; -.
PDBsum; 4X14; -.
PDBsum; 4X15; -.
PDBsum; 4X16; -.
PDBsum; 4X17; -.
ProteinModelPortal; P03089; -.
SMR; P03089; -.
GeneID; 1489518; -.
KEGG; vg:1489518; -.
KO; K19248; -.
OrthoDB; VOG090000AE; -.
EvolutionaryTrace; P03089; -.
Proteomes; UP000008478; Genome.
GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
GO; GO:0039620; C:T=7 icosahedral viral capsid; IEA:UniProtKB-KW.
GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
GO; GO:0075512; P:clathrin-dependent endocytosis of virus by host cell; IEA:UniProtKB-KW.
GO; GO:0019062; P:virion attachment to host cell; IEA:UniProtKB-KW.
Gene3D; 2.60.175.10; -; 1.
InterPro; IPR000662; Capsid_VP1_Polyomavir.
InterPro; IPR011222; dsDNA_vir_gr_I_capsid.
InterPro; IPR036931; Polyomavir_VP1_sf.
Pfam; PF00718; Polyoma_coat; 1.
PIRSF; PIRSF003376; Capsid_VP1_Polyomavir; 1.
SUPFAM; SSF88648; SSF88648; 1.
1: Evidence at protein level;
3D-structure; Alternative initiation; Alternative splicing;
Capsid protein; Clathrin-mediated endocytosis of virus by host;
Complete proteome; Disulfide bond; Host nucleus;
Host-virus interaction; Late protein; Phosphoprotein;
Reference proteome; T=7 icosahedral capsid protein;
Viral attachment to host cell; Viral penetration into host cytoplasm;
Virion; Virus endocytosis by host; Virus entry into host cell.
CHAIN 1 354 Major capsid protein VP1.
/FTId=PRO_0000115021.
REGION 294 354 Intrinsically disordered. {ECO:0000250}.
MOD_RES 330 330 Phosphothreonine; by host. {ECO:0000250}.
DISULFID 97 97 Interchain (with C-97). {ECO:0000250}.
VARIANT 66 66 D -> H (in strain: Isolate MAD11-BR).
VARIANT 74 74 N -> S (in strain: Isolate NY-1B, Isolate
N1 and Isolate G3).
VARIANT 75 75 R -> K (in strain: Isolate YI, Isolate
TKY-2A, Isolate MAD8-BR, Isolate HER1-BR,
Isolate NY-1B, Isolate N1, Isolate N4,
Isolate G3, Isolate C1, Isolate CY,
Isolate MY, Isolate AIC-1A and Isolate
Tokyo-1).
VARIANT 113 113 I -> L (in strain: Isolate YI, Isolate
C1, Isolate AIC-1A and Isolate Tokyo-1).
VARIANT 117 117 S -> T (in strain: Isolate YI, Isolate
TKY-2A, Isolate MAD8-BR, Isolate N4,
Isolate C1, Isolate CY, Isolate MY,
Isolate AIC-1A and Isolate Tokyo-1).
VARIANT 128 128 T -> A (in strain: Isolate MAD8-BR,
Isolate NY-1B, Isolate N1, Isolate G3 and
Isolate N4).
VARIANT 158 158 L -> V (in strain: Isolate YI, Isolate
TKY-2A, Isolate MAD8-BR, Isolate NY-1B,
Isolate N1, Isolate N4, Isolate G3,
Isolate C1, Isolate CY, Isolate MY,
Isolate AIC-1A and Isolate Tokyo-1).
VARIANT 267 267 S -> L (in strain: Isolate HER1-BR).
VARIANT 269 269 S -> F (in strain: Isolate MAD8-BR).
VARIANT 269 269 S -> T (in strain: Isolate YI).
VARIANT 269 269 S -> Y (in strain: Isolate TKY-2A).
VARIANT 321 321 V -> I (in strain: Isolate C1).
VARIANT 345 345 K -> R (in strain: Isolate YI, Isolate
TKY-2A, Isolate MAD8-BR, Isolate N1,
Isolate N4, Isolate G4, Isolate C1,
Isolate CY, Isolate MY, Isolate AIC-1A
and Isolate Tokyo-1).
STRAND 27 30 {ECO:0000244|PDB:4X17}.
HELIX 34 36 {ECO:0000244|PDB:4X17}.
STRAND 37 44 {ECO:0000244|PDB:4X17}.
STRAND 65 68 {ECO:0000244|PDB:4X17}.
HELIX 75 77 {ECO:0000244|PDB:4X17}.
STRAND 82 87 {ECO:0000244|PDB:4X17}.
STRAND 101 113 {ECO:0000244|PDB:4X17}.
HELIX 115 119 {ECO:0000244|PDB:4X17}.
STRAND 122 125 {ECO:0000244|PDB:4X17}.
STRAND 127 129 {ECO:0000244|PDB:4X17}.
STRAND 137 139 {ECO:0000244|PDB:4X17}.
STRAND 141 150 {ECO:0000244|PDB:4X17}.
STRAND 153 156 {ECO:0000244|PDB:4X17}.
HELIX 177 180 {ECO:0000244|PDB:4X17}.
STRAND 187 189 {ECO:0000244|PDB:4X17}.
TURN 193 195 {ECO:0000244|PDB:4JCE}.
HELIX 198 200 {ECO:0000244|PDB:4X17}.
STRAND 201 203 {ECO:0000244|PDB:4X17}.
STRAND 211 218 {ECO:0000244|PDB:4X17}.
STRAND 226 232 {ECO:0000244|PDB:4X17}.
HELIX 248 250 {ECO:0000244|PDB:4X17}.
STRAND 251 265 {ECO:0000244|PDB:4X17}.
STRAND 270 274 {ECO:0000244|PDB:4X17}.
STRAND 276 288 {ECO:0000244|PDB:4X17}.
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


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