CAPSD_BPQBE
ID CAPSD_BPQBE Reviewed; 133 AA.
AC P03615; D0U1F3; G4WZR7; Q774G0;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=Capsid protein;
DE Short=CP;
DE AltName: Full=Coat protein;
OS Escherichia virus Qbeta (Bacteriophage Q-beta).
OC Viruses; Riboviria; Orthornavirae; Lenarviricota; Leviviricetes;
OC Levivirales; Leviviridae; Allolevivirus.
OX NCBI_TaxID=39803;
OH NCBI_TaxID=562; Escherichia coli.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=7506687; DOI=10.1016/0378-1119(93)90261-z;
RA Kozlovska T.M., Cielens I., Dreilinna D., Dislers A., Baumanis V., Ose V.,
RA Pumpens P.;
RT "Recombinant RNA phage Q-beta capsid particles synthesized and self-
RT assembled in Escherichia coli.";
RL Gene 137:133-137(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=14667253; DOI=10.1186/1471-2148-3-24;
RA Bacher J.M., Bull J.J., Ellington A.D.;
RT "Evolution of phage with chemically ambiguous proteomes.";
RL BMC Evol. Biol. 3:24-24(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RC STRAIN=QB_1, QB_2 {ECO:0000312|EMBL:ACY07228.1},
RC QB_3 {ECO:0000312|EMBL:ACY07232.1}, and
RC QB_ancestral {ECO:0000312|EMBL:ACY07236.1};
RX PubMed=19956760; DOI=10.1371/journal.pgen.1000742;
RA Domingo-Calap P., Cuevas J.M., Sanjuan R.;
RT "The fitness effects of random mutations in single-stranded DNA and RNA
RT bacteriophages.";
RL PLoS Genet. 5:E1000742-E1000742(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RC STRAIN=Qbeta_1_FR {ECO:0000312|EMBL:AEQ25542.1},
RC Qbeta_2_FR {ECO:0000312|EMBL:AEQ25546.1}, and
RC Qbeta_3_FR {ECO:0000312|EMBL:AEQ25550.1};
RX PubMed=21967437; DOI=10.1111/j.1558-5646.2011.01339.x;
RA Domingo-Calap P., Sanjuan R.;
RT "Experimental evolution of RNA versus DNA viruses.";
RL Evolution 65:2987-2994(2011).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RC STRAIN=QB_ancestral {ECO:0000312|EMBL:BAP18764.1}, and TW18;
RX PubMed=25056887; DOI=10.1128/jvi.01127-14;
RA Kashiwagi A., Sugawara R., Sano-Tsushima F., Kumagai T., Yomo T.;
RT "Contribution of silent mutations to thermal adaptation of RNA
RT bacteriophage Qbeta.";
RL J. Virol. 88:11459-11468(2014).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1-81.
RX PubMed=361741; DOI=10.1016/s0021-9258(17)34304-1;
RA Escarmis C., Sastry P.A., Billeter M.A.;
RT "Determination of the first half of the coat protein cistron of
RT bacteriophage Q-beta as an application of a mapping procedure for RNA
RT fragments.";
RL J. Biol. Chem. 253:8390-8399(1978).
RN [7]
RP SEQUENCE REVISION TO 1-61.
RX PubMed=838709; DOI=10.1016/s0021-9258(19)75196-5;
RA Stoll E., Wilson K.J., Reiser J., Weissmann C.;
RT "Revised amino acid sequence of Qbeta coat protein between positions 1 and
RT 60.";
RL J. Biol. Chem. 252:990-993(1977).
RN [8]
RP PROTEIN SEQUENCE OF 2-133.
RX PubMed=5570434; DOI=10.1016/s0021-9258(18)61963-5;
RA Maita T., Konigsberg W.;
RT "The amino acid sequence of the Q-beta coat protein.";
RL J. Biol. Chem. 246:5003-5024(1971).
RN [9]
RP RNA-BINDING, FUNCTION, MUTAGENESIS OF VAL-33; THR-50; SER-57; ARG-60;
RP ASN-62; LYS-64; TYR-90 AND SER-96, AND SUBUNIT.
RX PubMed=8943226; DOI=10.1074/jbc.271.50.31839;
RA Lim F., Spingola M., Peabody D.S.;
RT "The RNA-binding site of bacteriophage Qbeta coat protein.";
RL J. Biol. Chem. 271:31839-31845(1996).
RN [10]
RP RNA-BINDING, AND SUBUNIT.
RX PubMed=16531233; DOI=10.1016/j.str.2005.12.006;
RA Horn W.T., Tars K., Grahn E., Helgstrand C., Baron A.J., Lago H.,
RA Adams C.J., Peabody D.S., Phillips S.E., Stonehouse N.J., Liljas L.,
RA Stockley P.G.;
RT "Structural basis of RNA binding discrimination between bacteriophages
RT Qbeta and MS2.";
RL Structure 14:487-495(2006).
RN [11]
RP FUNCTION.
RX PubMed=19913556; DOI=10.1016/j.jmb.2009.11.018;
RA Basnak G., Morton V.L., Rolfsson O., Stonehouse N.J., Ashcroft A.E.,
RA Stockley P.G.;
RT "Viral genomic single-stranded RNA directs the pathway toward a T=3
RT capsid.";
RL J. Mol. Biol. 395:924-936(2010).
RN [12]
RP INTERACTION WITH MATURATION PROTEIN A2.
RX PubMed=28111107; DOI=10.1016/j.jmb.2017.01.012;
RA Rumnieks J., Tars K.;
RT "Crystal structure of the maturation protein from bacteriophage Qbeta.";
RL J. Mol. Biol. 429:688-696(2017).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS).
RX PubMed=8736553; DOI=10.1016/s0969-2126(96)00060-3;
RA Golmohammadi R., Fridborg K., Bundule M., Valegard K., Liljas L.;
RT "The crystal structure of bacteriophage Q-beta at 3.5-A resolution.";
RL Structure 4:543-554(1996).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 2-133, AND RNA-BINDING.
RX PubMed=24035813; DOI=10.1016/j.jmb.2013.08.025;
RA Rumnieks J., Tars K.;
RT "Crystal structure of the bacteriophage Qbeta coat protein in complex with
RT the RNA operator of the replicase gene.";
RL J. Mol. Biol. 426:1039-1049(2014).
RN [15]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.70 ANGSTROMS) OF THE VIRION, FUNCTION,
RP AND SUBCELLULAR LOCATION.
RX PubMed=27671640; DOI=10.1073/pnas.1609482113;
RA Gorzelnik K.V., Cui Z., Reed C.A., Jakana J., Young R., Zhang J.;
RT "Asymmetric cryo-EM structure of the canonical Allolevivirus Qbeta reveals
RT a single maturation protein and the genomic ssRNA in situ.";
RL Proc. Natl. Acad. Sci. U.S.A. 113:11519-11524(2016).
RN [16]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.30 ANGSTROMS), INTERACTION WITH
RP MATURATION PROTEIN A2, AND SUBCELLULAR LOCATION.
RX PubMed=29078304; DOI=10.1073/pnas.1707102114;
RA Cui Z., Gorzelnik K.V., Chang J.Y., Langlais C., Jakana J., Young R.,
RA Zhang J.;
RT "Structures of Qbeta virions, virus-like particles, and the Qbeta-MurA
RT complex reveal internal coat proteins and the mechanism of host lysis.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:11697-11702(2017).
CC -!- FUNCTION: Capsid protein self-assembles to form an icosahedral capsid
CC with a T=3 symmetry, about 26 nm in diameter, and consisting of 89
CC capsid proteins dimers (178 capsid proteins) (PubMed:27671640,
CC PubMed:19913556). Involved in viral genome encapsidation through the
CC interaction between a capsid protein dimer and the multiple packaging
CC signals present in the RNA genome (PubMed:8943226, PubMed:27671640).
CC Binding of the capsid proteins to the viral RNA induces a
CC conformational change required for efficient T=3 shell formation
CC (PubMed:19913556). The capsid contains also 1 copy of the A2 maturation
CC protein (PubMed:27671640). {ECO:0000269|PubMed:19913556,
CC ECO:0000269|PubMed:27671640, ECO:0000269|PubMed:8943226}.
CC -!- FUNCTION: Acts as a translational repressor of viral replicase
CC synthesis late in infection. This latter function is the result of
CC capsid protein interaction with an RNA hairpin which contains the
CC replicase ribosome-binding site. {ECO:0000269|PubMed:8943226}.
CC -!- SUBUNIT: Homodimer (PubMed:16531233). The homodimers binds to the viral
CC RNA via an operator hairpin, but also to many other RNA sequences in
CC the viral genome; this interaction probably shifts the virus from the
CC replicative to the assembly phase and ensures specific encapsidation of
CC the viral genome (PubMed:8943226, PubMed:16531233). Interacts with the
CC maturation protein A2 (PubMed:28111107, PubMed:29078304).
CC {ECO:0000269|PubMed:16531233, ECO:0000269|PubMed:28111107,
CC ECO:0000269|PubMed:29078304, ECO:0000269|PubMed:8943226}.
CC -!- SUBCELLULAR LOCATION: Virion {ECO:0000269|PubMed:27671640,
CC ECO:0000269|PubMed:29078304}. Note=The shell is composed of 89 dimers
CC of the capsid protein, one of them being sequestered inside the virion,
CC and 1 copy of the maturation protein. {ECO:0000269|PubMed:27671640,
CC ECO:0000269|PubMed:29078304}.
CC -!- WEB RESOURCE: Name=Virus Particle ExploreR db; Note=Icosahedral capsid
CC structure;
CC URL="https://viperdb.scripps.edu/Info_Page.php?VDB=1qbe";
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DR EMBL; M99039; AAA16662.1; -; Unassigned_DNA.
DR EMBL; AY099114; AAM33126.1; -; Genomic_RNA.
DR EMBL; GQ153928; ACY07224.1; -; Genomic_RNA.
DR EMBL; GQ153929; ACY07228.1; -; Genomic_RNA.
DR EMBL; GQ153930; ACY07232.1; -; Genomic_RNA.
DR EMBL; GQ153931; ACY07236.1; -; Genomic_RNA.
DR EMBL; JF719735; AEQ25542.1; -; Genomic_RNA.
DR EMBL; JF719736; AEQ25546.1; -; Genomic_RNA.
DR EMBL; JF719737; AEQ25550.1; -; Genomic_RNA.
DR EMBL; AB971354; BAP18764.1; -; Genomic_RNA.
DR EMBL; V00643; CAA23992.1; -; mRNA.
DR PIR; A92240; VCBPQB.
DR PDB; 1QBE; X-ray; 3.50 A; A/B/C=2-133.
DR PDB; 4L8H; X-ray; 2.40 A; A/B=2-133.
DR PDB; 5KIP; EM; 3.70 A; A/B/C=1-133.
DR PDB; 5VLY; EM; 3.30 A; A/B/C=1-133.
DR PDB; 5VLZ; EM; 4.40 A; AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/BA/BB/BC/BD/BE/BF/BG/BH/BI/BJ/BK/BL/BM/BN/CA/CB=1-133.
DR PDB; 7LGE; EM; 5.60 A; A/B/C/D=1-133.
DR PDB; 7LGF; EM; 6.10 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U=1-133.
DR PDB; 7LGG; EM; 6.20 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O=1-133.
DR PDB; 7LGH; EM; 8.90 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V=1-133.
DR PDB; 7LHD; EM; 4.60 A; B/BA/BB/BC/BD/BE/BF/BG/BH/BI/BJ/BK/BL/BM/BN/CA/CB/CC/CD/CE/CF/CG/CH/CI/CJ/CK/CL/CM/CN/D=1-133.
DR PDBsum; 1QBE; -.
DR PDBsum; 4L8H; -.
DR PDBsum; 5KIP; -.
DR PDBsum; 5VLY; -.
DR PDBsum; 5VLZ; -.
DR PDBsum; 7LGE; -.
DR PDBsum; 7LGF; -.
DR PDBsum; 7LGG; -.
DR PDBsum; 7LGH; -.
DR PDBsum; 7LHD; -.
DR SMR; P03615; -.
DR EvolutionaryTrace; P03615; -.
DR Proteomes; UP000185268; Genome.
DR Proteomes; UP000305125; Genome.
DR Proteomes; UP000306921; Genome.
DR Proteomes; UP000309733; Genome.
DR GO; GO:0039617; C:T=3 icosahedral viral capsid; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR GO; GO:0030371; F:translation repressor activity; IMP:UniProtKB.
DR Gene3D; 3.30.380.10; -; 1.
DR InterPro; IPR002703; Levivir_coat.
DR InterPro; IPR015954; Phage_RNA-type_capsid.
DR Pfam; PF01819; Levi_coat; 1.
DR SUPFAM; SSF55405; SSF55405; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Capsid protein; Direct protein sequencing;
KW Reference proteome; RNA-binding; T=3 icosahedral capsid protein;
KW Translation regulation; Virion.
FT INIT_MET 1
FT /note="Removed; by host"
FT /evidence="ECO:0000269|PubMed:5570434"
FT CHAIN 2..133
FT /note="Capsid protein"
FT /id="PRO_0000164846"
FT SITE 90
FT /note="RNA-binding"
FT /evidence="ECO:0000269|PubMed:24035813"
FT VARIANT 34
FT /note="A -> S (in strain: Qbeta_3_FR)"
FT /evidence="ECO:0000269|PubMed:21967437"
FT VARIANT 76
FT /note="T -> A (in strain: QB_1 and Qbeta_1_FR)"
FT /evidence="ECO:0000269|PubMed:19956760,
FT ECO:0000269|PubMed:21967437"
FT MUTAGEN 33
FT /note="V->A: Decreased RNA-binding to the viral operator
FT and loss of repressor activity."
FT /evidence="ECO:0000269|PubMed:8943226"
FT MUTAGEN 50
FT /note="T->A: Decreased RNA-binding to the viral operator
FT and loss of repressor activity."
FT /evidence="ECO:0000269|PubMed:8943226"
FT MUTAGEN 57
FT /note="S->P: Decreased RNA-binding to the viral operator
FT and loss of repressor activity."
FT /evidence="ECO:0000269|PubMed:8943226"
FT MUTAGEN 60
FT /note="R->C: Decreased RNA-binding to the viral operator
FT and loss of repressor activity."
FT /evidence="ECO:0000269|PubMed:8943226"
FT MUTAGEN 62
FT /note="N->D: Decreased RNA-binding to the viral operator
FT and loss of repressor activity."
FT /evidence="ECO:0000269|PubMed:8943226"
FT MUTAGEN 64
FT /note="K->E: Decreased RNA-binding to the viral operator
FT and loss of repressor activity."
FT /evidence="ECO:0000269|PubMed:8943226"
FT MUTAGEN 90
FT /note="Y->H: Decreased RNA-binding to the viral operator
FT and loss of repressor activity."
FT /evidence="ECO:0000269|PubMed:8943226"
FT MUTAGEN 96
FT /note="S->L: Decreased RNA-binding to the viral operator
FT and loss of repressor activity."
FT /evidence="ECO:0000269|PubMed:8943226"
FT CONFLICT 23
FT /note="N -> D (in Ref. 8; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 57
FT /note="Missing (in Ref. 8; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 7..12
FT /evidence="ECO:0007829|PDB:4L8H"
FT TURN 13..16
FT /evidence="ECO:0007829|PDB:4L8H"
FT STRAND 18..27
FT /evidence="ECO:0007829|PDB:4L8H"
FT TURN 29..31
FT /evidence="ECO:0007829|PDB:4L8H"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:4L8H"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:1QBE"
FT STRAND 48..54
FT /evidence="ECO:0007829|PDB:4L8H"
FT STRAND 62..73
FT /evidence="ECO:0007829|PDB:4L8H"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:1QBE"
FT STRAND 87..97
FT /evidence="ECO:0007829|PDB:4L8H"
FT HELIX 103..116
FT /evidence="ECO:0007829|PDB:4L8H"
FT HELIX 120..126
FT /evidence="ECO:0007829|PDB:4L8H"
SQ SEQUENCE 133 AA; 14254 MW; 1B7967F0256C31DE CRC64;
MAKLETVTLG NIGKDGKQTL VLNPRGVNPT NGVASLSQAG AVPALEKRVT VSVSQPSRNR
KNYKVQVKIQ NPTACTANGS CDPSVTRQAY ADVTFSFTQY STDEERAFVR TELAALLASP
LLIDAIDQLN PAY
