VP6_ROTRF
ID VP6_ROTRF Reviewed; 397 AA.
AC P04509;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Intermediate capsid protein VP6 {ECO:0000255|HAMAP-Rule:MF_04129};
OS Rotavirus A (strain RVA/Cow/France/RF/1975/G6P6[1]) (RV-A).
OC Viruses; Riboviria; Orthornavirae; Duplornaviricota; Resentoviricetes;
OC Reovirales; Reoviridae; Sedoreovirinae; Rotavirus; Rotavirus A.
OX NCBI_TaxID=10933;
OH NCBI_TaxID=9913; Bos taurus (Bovine).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=6093360; DOI=10.1016/0042-6822(84)90159-4;
RA Cohen J., Lefevre F., Estes M.K., Bremont M.;
RT "Cloning of bovine rotavirus (RF strain): nucleotide sequence of the gene
RT coding for the major capsid protein.";
RL Virology 138:178-182(1984).
RN [2]
RP SEQUENCE REVISION.
RA Cohen J.;
RL Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=6292454; DOI=10.1128/jvi.43.3.1113-1117.1982;
RA Bican P., Cohen J., Charpilienne A., Scherrer R.;
RT "Purification and characterization of bovine rotavirus cores.";
RL J. Virol. 43:1113-1117(1982).
RN [4]
RP INTERACTION WITH THE INNER CAPSID PROTEIN VP2, SUBCELLULAR LOCATION,
RP MUTAGENESIS OF GLN-32; LEU-65; LEU-70 AND LEU-71, AND FUNCTION.
RX PubMed=12097594; DOI=10.1128/jvi.76.15.7822-7831.2002;
RA Charpilienne A., Lepault J., Rey F.A., Cohen J.;
RT "Identification of rotavirus VP6 residues located at the interface with VP2
RT that are essential for capsid assembly and transcriptase activity.";
RL J. Virol. 76:7822-7831(2002).
RN [5]
RP ZINC-BINDING, AND MUTAGENESIS OF HIS-153.
RX PubMed=12610135; DOI=10.1128/jvi.77.6.3595-3601.2003;
RA Erk I., Huet J.-C., Duarte M., Duquerroy S., Rey F.A., Cohen J.,
RA Lepault J.;
RT "A zinc ion controls assembly and stability of the major capsid protein of
RT rotavirus.";
RL J. Virol. 77:3595-3601(2003).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH ZINC, SUBUNIT,
RP ZINC-BINDING, FUNCTION, INTERACTION WITH THE INNER CAPSID PROTEIN VP2,
RP INTERACTION WITH THE OUTER CAPSID GLYCOPROTEIN VP7, AND SUBCELLULAR
RP LOCATION.
RX PubMed=11285213; DOI=10.1093/emboj/20.7.1485;
RA Mathieu M., Petitpas I., Navaza J., Lepault J., Kohli E., Pothier P.,
RA Prasad B.V.V., Cohen J., Rey F.A.;
RT "Atomic structure of the major capsid protein of rotavirus: implications
RT for the architecture of the virion.";
RL EMBO J. 20:1485-1497(2001).
RN [7] {ECO:0007744|PDB:3GZU}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.80 ANGSTROMS), AND INTERACTION WITH THE
RP OUTER CAPSID GLYCOPROTEIN VP7.
RX PubMed=19487668; DOI=10.1073/pnas.0904024106;
RA Chen J.Z., Settembre E.C., Aoki S.T., Zhang X., Bellamy A.R.,
RA Dormitzer P.R., Harrison S.C., Grigorieff N.;
RT "Molecular interactions in rotavirus assembly and uncoating seen by high-
RT resolution cryo-EM.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:10644-10648(2009).
CC -!- FUNCTION: Intermediate capsid protein that self assembles to form an
CC icosahedral capsid with a T=13 symmetry, which consists of 230 trimers
CC of VP6, with channels at each of its five-fold vertices
CC (PubMed:11285213). This capsid constitutes the middle concentric layer
CC of the viral mature particle (PubMed:11285213). The innermost VP2
CC capsid and the intermediate VP6 capsid remain intact following cell
CC entry to protect the dsRNA from degradation and to prevent unfavorable
CC antiviral responses in the host cell during all the replication cycle
CC of the virus. Nascent transcripts are transcribed within the structural
CC confines of this double-layered particle (DLP) and are extruded through
CC the channels at the five-fold axes (By similarity). VP6 is required for
CC the transcription activity of the DLP (PubMed:12097594).
CC {ECO:0000255|HAMAP-Rule:MF_04129, ECO:0000269|PubMed:11285213,
CC ECO:0000269|PubMed:12097594, ECO:0000269|PubMed:6292454}.
CC -!- SUBUNIT: Homotrimer (PubMed:11285213). Interacts with the inner capsid
CC protein VP2 (PubMed:12097594, PubMed:11285213). Interacts with the
CC outer capsid glycoprotein VP7 (PubMed:11285213, PubMed:19487668).
CC Interacts with the outer capsid protein VP5* (By similarity).
CC {ECO:0000255|HAMAP-Rule:MF_04129, ECO:0000269|PubMed:11285213,
CC ECO:0000269|PubMed:12097594, ECO:0000269|PubMed:19487668}.
CC -!- SUBCELLULAR LOCATION: Virion {ECO:0000255|HAMAP-Rule:MF_04129,
CC ECO:0000269|PubMed:11285213, ECO:0000269|PubMed:12097594}.
CC Note=Component of the intermediate capsid (PubMed:11285213). Also found
CC in spherical cytoplasmic structures, called virus factories, that
CC appear early after infection and are the site of viral replication and
CC packaging (Potential). {ECO:0000255|HAMAP-Rule:MF_04129,
CC ECO:0000269|PubMed:11285213}.
CC -!- PTM: The N-terminus is blocked. {ECO:0000255|HAMAP-Rule:MF_04129,
CC ECO:0000269|PubMed:12610135}.
CC -!- PTM: Sumoylated with SUMO1 and SUMO2. Sumoylation of viral proteins
CC seems to have a positive role on viral replication. {ECO:0000255|HAMAP-
CC Rule:MF_04129}.
CC -!- MISCELLANEOUS: The VP6 trimer contains a zinc ion located at the center
CC of the molecule (PubMed:11285213). The zinc ion is not essential for
CC either trimerization or transcription activity of the DLP. Zinc-
CC depleted VP6 has an increased sensitivity to proteases
CC (PubMed:12610135). {ECO:0000255|HAMAP-Rule:MF_04129,
CC ECO:0000269|PubMed:11285213, ECO:0000269|PubMed:12610135}.
CC -!- SIMILARITY: Belongs to the rotavirus VP6 family. {ECO:0000255|HAMAP-
CC Rule:MF_04129, ECO:0000305}.
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DR EMBL; K02254; AAC98425.1; -; Genomic_RNA.
DR PIR; A04132; VPXRBR.
DR PDB; 1QHD; X-ray; 1.95 A; A=1-397.
DR PDB; 3GZU; EM; -; C/D/E/F/G/H/I/J/K/L/M/N/O=1-397.
DR PDB; 3J9S; EM; 2.60 A; A=1-397.
DR PDBsum; 1QHD; -.
DR PDBsum; 3GZU; -.
DR PDBsum; 3J9S; -.
DR SMR; P04509; -.
DR EvolutionaryTrace; P04509; -.
DR Proteomes; UP000007179; Genome.
DR GO; GO:0039621; C:T=13 icosahedral viral capsid; IDA:UniProtKB.
DR GO; GO:0019031; C:viral envelope; IEA:UniProtKB-UniRule.
DR GO; GO:0039626; C:viral intermediate capsid; IDA:UniProtKB.
DR GO; GO:0046789; F:host cell surface receptor binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0005198; F:structural molecule activity; IEA:UniProtKB-UniRule.
DR GO; GO:0019064; P:fusion of virus membrane with host plasma membrane; IEA:UniProtKB-UniRule.
DR HAMAP; MF_04126; Rota_VP6; 1.
DR HAMAP; MF_04129; Rota_VP6_A; 1.
DR InterPro; IPR008980; Capsid_hemagglutn.
DR InterPro; IPR001385; Rotavirus_A/C_VP6.
DR InterPro; IPR008935; Virus_capsid_a-hlx_vir.
DR Pfam; PF00980; Rota_Capsid_VP6; 1.
DR SUPFAM; SSF48345; SSF48345; 1.
DR SUPFAM; SSF49818; SSF49818; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Capsid protein; Intermediate capsid protein;
KW Metal-binding; Ubl conjugation; Virion; Zinc.
FT CHAIN 1..397
FT /note="Intermediate capsid protein VP6"
FT /id="PRO_0000149561"
FT REGION 62..73
FT /note="Interaction with the inner capsid protein VP2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04129"
FT BINDING 153
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between all trimeric partners"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04129,
FT ECO:0000269|PubMed:11285213"
FT BINDING 266
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04129,
FT ECO:0000269|PubMed:11285213"
FT BINDING 286
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04129,
FT ECO:0000269|PubMed:11285213"
FT MUTAGEN 32
FT /note="Q->E: Complete loss of in vitro DLP transcription
FT activity, no effect on particle assembly."
FT /evidence="ECO:0000269|PubMed:12097594"
FT MUTAGEN 65
FT /note="L->D: Loss of in vitro DLP transcriptase activity,
FT no effect on particle assembly; when associated with A-70
FT or N-70. Loss of in vitro DLP assembly and transcriptase
FT activity, and almost complete loss of interaction with VP2;
FT when associated with N-71."
FT /evidence="ECO:0000269|PubMed:12097594"
FT MUTAGEN 70
FT /note="L->A: Loss of in vitro DLP transcriptase activity,
FT no effect on particle assembly; when associated with D-65."
FT /evidence="ECO:0000269|PubMed:12097594"
FT MUTAGEN 70
FT /note="L->N: Loss of in vitro DLP assembly and
FT transcriptase activity, and almost complete loss of
FT interaction with VP2; when associated with N-71. Loss of in
FT vitro DLP transcriptase activity, no effect on particle
FT assembly; when associated with D-65."
FT /evidence="ECO:0000269|PubMed:12097594"
FT MUTAGEN 71
FT /note="L->N: Loss of in vitro DLP assembly and
FT transcriptase activity, and almost complete loss of
FT interaction with VP2; when associated with D-65 or N-70."
FT /evidence="ECO:0000269|PubMed:12097594"
FT MUTAGEN 153
FT /note="H->S: Impaired homotrimer formation at pH above 7.0.
FT No effect on transcription activity or on VP2-VP6
FT interaction."
FT /evidence="ECO:0000269|PubMed:12610135"
FT HELIX 2..17
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 28..41
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 45..48
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 75..100
FT /evidence="ECO:0007829|PDB:1QHD"
FT TURN 105..109
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 114..119
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 122..127
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 134..143
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 150..154
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 158..168
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 177..185
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 187..194
FT /evidence="ECO:0007829|PDB:1QHD"
FT TURN 195..200
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 205..227
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 236..239
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 246..249
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 251..253
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 257..265
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 268..275
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 278..295
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 302..305
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 316..333
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 342..352
FT /evidence="ECO:0007829|PDB:1QHD"
FT STRAND 359..361
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 363..365
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 367..372
FT /evidence="ECO:0007829|PDB:1QHD"
FT HELIX 376..392
FT /evidence="ECO:0007829|PDB:1QHD"
FT TURN 393..395
FT /evidence="ECO:0007829|PDB:1QHD"
SQ SEQUENCE 397 AA; 44843 MW; 86CD8739452CA4A7 CRC64;
MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG IGNLPIRNWN
FDFGLLGTTL LNLDANYVET ARNTIDYFVD FVDNVCMDEM VRESQRNGIA PQSDSLIKLS
GIKFKRINFD NSSEYIENWN LQNRRQRTGF TFHKPNIFPY SASFTLNRSQ PAHDNLMGTM
WLNAGSEIQV AGFDYSCAIN APANTQQFEH IVQLRRVLTT ATITLLPDAE RFSFPRVITS
ADGATTWYFN PVILRPNNVE IEFLLNGQII NTYQARFGTI IARNFDTIRL SFQLMRPPNM
TPAVAALFPN AQPFEHHATV GLTLRIESAV CESVLADASE TMLANVTSVR QEYAIPVGPV
FPPGMNWTDL ITNYSPSRED NLQRVFTVAS IRSMLVK
