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 24-JAN-2024, entry version 109. 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 Norzivirales; Fiersviridae; Qubevirus. 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}, QB_3 RC {ECO:0000312|EMBL:ACY07232.1}, and QB_ancestral RC {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}, Qbeta_2_FR RC {ECO:0000312|EMBL:AEQ25546.1}, and Qbeta_3_FR RC {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 -!- SIMILARITY: Belongs to the Leviviricetes capsid protein family. CC {ECO:0000305}. CC -!- WEB RESOURCE: Name=Virus Particle ExploreR db; Note=Icosahedral capsid CC structure; CC URL="https://viperdb.scripps.edu/Info_Page.php?VDB=1qbe"; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 EMDB; EMD-23321; -. DR EMDB; EMD-23322; -. DR EMDB; EMD-23323; -. DR EMDB; EMD-23324; -. DR EMDB; EMD-23336; -. DR EMDB; EMD-8253; -. DR EMDB; EMD-8708; -. DR EMDB; EMD-8709; -. DR SMR; P03615; -. DR EvolutionaryTrace; P03615; -. DR Proteomes; UP000185268; Segment. DR Proteomes; UP000305125; Segment. DR Proteomes; UP000306921; Segment. DR Proteomes; UP000309733; Segment. 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; MS2 Viral Coat Protein; 1. DR InterPro; IPR002703; Levivir_coat. DR InterPro; IPR015954; Phage_RNA-type_capsid. DR Pfam; PF01819; Levi_coat; 1. DR SUPFAM; SSF55405; RNA bacteriophage capsid protein; 1. PE 1: Evidence at protein level; KW 3D-structure; Capsid protein; Direct protein sequencing; RNA-binding; KW T=3 icosahedral capsid protein; 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 //