ID   POL2_BPMV               Reviewed;        1018 AA.
AC   P23009;
DT   01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-1992, sequence version 2.
DT   27-MAR-2024, entry version 125.
DE   RecName: Full=RNA2 polyprotein;
DE   AltName: Full=Genome polyprotein M;
DE   AltName: Full=M RNA polyprotein;
DE   AltName: Full=Middle component RNA polyprotein;
DE   AltName: Full=P2;
DE   Contains:
DE     RecName: Full=VP58;
DE     AltName: Full=P58;
DE   Contains:
DE     RecName: Full=Movement protein;
DE              Short=MP;
DE   Contains:
DE     RecName: Full=Large capsid protein;
DE              Short=LCP;
DE     AltName: Full=Coat protein VP42;
DE     AltName: Full=L subunit;
DE     AltName: Full=Large coat protein;
DE   Contains:
DE     RecName: Full=Small capsid protein precursor;
DE     AltName: Full=S subunit;
DE   Contains:
DE     RecName: Full=Mature small capsid protein;
DE              Short=SCP;
DE     AltName: Full=Coat protein VP22;
DE     AltName: Full=Small capsid protein, N-terminus part;
DE     AltName: Full=Small coat protein, N-terminus part;
DE   Contains:
DE     RecName: Full=Small capsid protein C-terminus part;
DE     AltName: Full=Small coat protein C-terminus part;
OS   Bean-pod mottle virus (strain Kentucky G7) (BPMV).
OC   Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC   Picornavirales; Secoviridae; Comovirinae; Comovirus; Comovirus siliquae.
OX   NCBI_TaxID=31715;
OH   NCBI_TaxID=53866; Desmodium.
OH   NCBI_TaxID=3847; Glycine max (Soybean) (Glycine hispida).
OH   NCBI_TaxID=3885; Phaseolus vulgaris (Kidney bean) (French bean).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=2053290; DOI=10.1016/0042-6822(91)90155-5;
RA   Macfarlane S.A., Shanks M., Davies J.W., Zlotnick A., Lomonossoff G.P.;
RT   "Analysis of the nucleotide sequence of bean pod mottle virus middle
RT   component RNA.";
RL   Virology 183:405-409(1991).
RN   [2]
RP   POSSIBLE PROTEOLYTIC CLEAVAGE (SMALL CAPSID PROTEIN PRECURSOR).
RX   PubMed=1716655; DOI=10.1099/0022-1317-72-9-2225;
RA   Joisson C., Van Regenmortel M.H.;
RT   "Influence of the C terminus of the small protein subunit of bean pod
RT   mottle virus on the antigenicity of the virus determined using monoclonal
RT   antibodies and anti-peptide antiserum.";
RL   J. Gen. Virol. 72:2225-2232(1991).
RN   [3]
RP   ALTERNATIVE INITIATION, AND FUNCTION (VP58).
RX   PubMed=24390330; DOI=10.1128/jvi.03301-13;
RA   Lin J., Guo J., Finer J., Dorrance A.E., Redinbaugh M.G., Qu F.;
RT   "The bean pod mottle virus RNA2-encoded 58-kilodalton protein P58 is
RT   required in cis for RNA2 accumulation.";
RL   J. Virol. 88:3213-3222(2014).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 447-1018, FUNCTION (LARGE CAPSID
RP   PROTEIN), FUNCTION (MATURE SMALL CAPSID PROTEIN), SUBCELLULAR LOCATION
RP   (LARGE CAPSID PROTEIN), AND SUBCELLULAR LOCATION (MATURE SMALL CAPSID
RP   PROTEIN).
RX   PubMed=2749253; DOI=10.1126/science.2749253;
RA   Chen Z., Stauffacher C., Li Y., Schmidt T., Bomu W., Kamer G., Shanks M.,
RA   Lomonossoff G., Johnson J.E.;
RT   "Protein-RNA interactions in an icosahedral virus at 3.0-A resolution.";
RL   Science 245:154-159(1989).
RN   [5]
RP   X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 447-1005, FUNCTION (LARGE CAPSID
RP   PROTEIN), FUNCTION (MATURE SMALL CAPSID PROTEIN), SUBCELLULAR LOCATION
RP   (LARGE CAPSID PROTEIN), AND SUBCELLULAR LOCATION (MATURE SMALL CAPSID
RP   PROTEIN).
RX   PubMed=14517057; DOI=10.1016/s0042-6822(03)00457-4;
RA   Lin T., Cavarelli J., Johnson J.E.;
RT   "Evidence for assembly-dependent folding of protein and RNA in an
RT   icosahedral virus.";
RL   Virology 314:26-33(2003).
CC   -!- FUNCTION: [VP58]: Responsible for viral RNA2 accumulation. May function
CC       by recruiting the RNA1-encoded polyprotein that contains the
CC       replication protein to RNA2 and enable its replication.
CC       {ECO:0000269|PubMed:24390330}.
CC   -!- FUNCTION: [Movement protein]: Transports the viral genome to
CC       neighboring plant cells directly through plasmosdesmata, without any
CC       budding. The movement protein allows efficient cell to cell
CC       propagation, by bypassing the host cell wall barrier. Acts by forming a
CC       tubular structure at the host plasmodesmata, enlarging it enough to
CC       allow free passage of virion capsids. Binds to GTP and to single-
CC       stranded RNA and single-stranded DNA in a non-sequence-specific manner.
CC       {ECO:0000250|UniProtKB:P03599}.
CC   -!- FUNCTION: [Small capsid protein precursor]: The cleavable C-terminus of
CC       small capsid protein seems to be involved in viral assembly and RNA
CC       packaging. After virus assembly, these amino acids are cleaved off
CC       during the normal maturation of the virus. Also seems to act as
CC       suppressor of post-transcriptional gene silencing (PTGS), a mechanism
CC       of plant viral defense that limits the accumulation of viral RNAs.
CC       {ECO:0000250|UniProtKB:P03599}.
CC   -!- FUNCTION: [Small capsid protein C-terminus part]: Acts as a suppressor
CC       of RNA-mediated gene silencing, also known as post-transcriptional gene
CC       silencing (PTGS), a mechanism of plant viral defense that limits the
CC       accumulation of viral RNAs. {ECO:0000250|UniProtKB:P03599}.
CC   -!- FUNCTION: [Large capsid protein]: Together with the mature small capsid
CC       protein, forms an icosahedral capsid (T=3) enclosing the viral positive
CC       strand RNA genome, with a diameter of approximately 300 Angstroms. The
CC       capsid is formed from 60 copies each of the large and the mature small
CC       capsid protein. The large capsid protein interacts with the viral RNA.
CC       {ECO:0000269|PubMed:14517057, ECO:0000269|PubMed:2749253}.
CC   -!- FUNCTION: [Mature small capsid protein]: Together with the large capsid
CC       protein, forms an icosahedral capsid (T=3) enclosing the viral positive
CC       strand RNA genome, with a diameter of approximately 300 Angstroms. The
CC       capsid is formed from 60 copies each of the large and the mature small
CC       capsid protein. The mature small capsid protein forms the turrets at
CC       the fivefold axes of the viral particle. {ECO:0000269|PubMed:14517057,
CC       ECO:0000269|PubMed:2749253}.
CC   -!- SUBUNIT: [Mature small capsid protein]: Interacts with the large capsid
CC       protein. {ECO:0000250|UniProtKB:P03599}.
CC   -!- SUBUNIT: [Large capsid protein]: Interacts with the small capsid
CC       protein. Homomultimer; assembles as pentons. Interacts with the
CC       movement protein (via C-terminus). {ECO:0000250|UniProtKB:P03599}.
CC   -!- SUBUNIT: [Movement protein]: Interacts (via C-terminus) with the large
CC       capsid protein. {ECO:0000250|UniProtKB:P03599}.
CC   -!- SUBCELLULAR LOCATION: [Movement protein]: Host cell junction, host
CC       plasmodesma {ECO:0000250|UniProtKB:P03599}. Note=Assembles in tubules
CC       that are embedded within modified plasmodesmata.
CC       {ECO:0000250|UniProtKB:P03599}.
CC   -!- SUBCELLULAR LOCATION: [Large capsid protein]: Virion
CC       {ECO:0000269|PubMed:14517057, ECO:0000269|PubMed:2749253}.
CC   -!- SUBCELLULAR LOCATION: [Mature small capsid protein]: Virion
CC       {ECO:0000269|PubMed:14517057, ECO:0000269|PubMed:2749253}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative initiation; Named isoforms=2;
CC       Name=1; Synonyms=RNA2 polyprotein;
CC         IsoId=P23009-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=P23009-2; Sequence=VSP_059980;
CC   -!- DOMAIN: [Small capsid protein precursor]: The C-terminus is required
CC       for efficient assembly and RNA packaging.
CC       {ECO:0000250|UniProtKB:P03599}.
CC   -!- DOMAIN: [Large capsid protein]: Contains a beta-sheet structure called
CC       beta-barrel jelly roll. {ECO:0000250|UniProtKB:P03599}.
CC   -!- DOMAIN: [Mature small capsid protein]: Contains a beta-sheet structure
CC       called beta-barrel jelly roll. {ECO:0000250|UniProtKB:P03599}.
CC   -!- DOMAIN: [Movement protein]: The C-terminus is involved in binding to
CC       the large capsid protein, and hence to the virion.
CC       {ECO:0000250|UniProtKB:P03599}.
CC   -!- PTM: [Small capsid protein precursor]: The C-terminal amino acids of
CC       the small capsid protein is specifically cleaved by the RNA1 encoded
CC       picornain 3C-like protease during maturation.
CC       {ECO:0000250|UniProtKB:P03599, ECO:0000305|PubMed:1716655}.
CC   -!- PTM: [RNA2 polyprotein]: Specific enzymatic cleavages by picornain 3C-
CC       like protease in vivo yield mature proteins.
CC       {ECO:0000250|UniProtKB:P03599}.
CC   -!- CAUTION: It is uncertain whether Met-1 or Met-103 is the initiator.
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=1pgl";
CC   -!- WEB RESOURCE: Name=Virus Particle ExploreR db; Note=Icosahedral capsid
CC       structure;
CC       URL="https://viperdb.scripps.edu/Info_Page.php?VDB=1pgw";
CC   -!- WEB RESOURCE: Name=Virus Particle ExploreR db; Note=Icosahedral capsid
CC       structure;
CC       URL="https://viperdb.scripps.edu/Info_Page.php?VDB=1bmv";
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DR   EMBL; M62738; AAA42801.1; -; Genomic_RNA.
DR   PIR; A40321; GNWXG7.
DR   RefSeq; NP_612348.1; NC_003495.1.
DR   PDB; 1BMV; X-ray; 3.00 A; 1=821-1005, 2=447-820.
DR   PDB; 1PGL; X-ray; 2.80 A; 1=821-1005, 2=447-816.
DR   PDB; 1PGW; X-ray; 2.90 A; 1=821-1005, 2=466-816.
DR   PDBsum; 1BMV; -.
DR   PDBsum; 1PGL; -.
DR   PDBsum; 1PGW; -.
DR   SMR; P23009; -.
DR   GeneID; 956616; -.
DR   KEGG; vg:956616; -.
DR   EvolutionaryTrace; P23009; -.
DR   Proteomes; UP000007610; Genome.
DR   GO; GO:0044219; C:host cell plasmodesma; IEA:UniProtKB-SubCell.
DR   GO; GO:0039617; C:T=3 icosahedral viral capsid; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR   GO; GO:0046740; P:transport of virus in host, cell to cell; IEA:UniProtKB-KW.
DR   Gene3D; 2.60.120.20; -; 2.
DR   InterPro; IPR003181; Como_LCP.
DR   InterPro; IPR003182; RNA2_polyprotein.
DR   InterPro; IPR029053; Viral_coat.
DR   Pfam; PF02247; Como_LCP; 1.
DR   Pfam; PF02248; Como_SCP; 1.
DR   SUPFAM; SSF88633; Positive stranded ssRNA viruses; 3.
PE   1: Evidence at protein level;
KW   3D-structure; Alternative initiation; Capsid protein; DNA-binding;
KW   GTP-binding; Host cell junction; Host-virus interaction;
KW   Inhibition of host innate immune response by virus; Nucleotide-binding;
KW   RNA-binding; Suppressor of RNA silencing; T=3 icosahedral capsid protein;
KW   Transport; Viral immunoevasion; Viral movement protein; Virion.
FT   CHAIN           1..1018
FT                   /note="RNA2 polyprotein"
FT                   /id="PRO_0000445846"
FT   CHAIN           1..446
FT                   /note="VP58"
FT                   /id="PRO_0000037031"
FT   CHAIN           103..446
FT                   /note="Movement protein"
FT                   /id="PRO_0000445847"
FT   CHAIN           447..820
FT                   /note="Large capsid protein"
FT                   /id="PRO_0000037032"
FT   CHAIN           821..1018
FT                   /note="Small capsid protein precursor"
FT                   /id="PRO_0000037033"
FT   CHAIN           821..1005
FT                   /note="Mature small capsid protein"
FT                   /id="PRO_0000445848"
FT   CHAIN           1006..1018
FT                   /note="Small capsid protein C-terminus part"
FT                   /id="PRO_0000445849"
FT   REGION          401..407
FT                   /note="Involved in tubule formation by the movement
FT                   protein"
FT                   /evidence="ECO:0000250|UniProtKB:P03599"
FT   SITE            446..447
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250|UniProtKB:P03599"
FT   SITE            463
FT                   /note="Interaction with the viral RNA"
FT                   /evidence="ECO:0000250|UniProtKB:P03599"
FT   SITE            819..820
FT                   /note="Cleavage; by viral protease"
FT                   /evidence="ECO:0000250|UniProtKB:P03599"
FT   SITE            1005..1006
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000305|PubMed:1716655"
FT   VAR_SEQ         1..102
FT                   /note="Missing (in isoform 2)"
FT                   /id="VSP_059980"
FT   HELIX           451..453
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   TURN            466..469
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          470..478
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          487..492
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   HELIX           493..496
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          498..500
FT                   /evidence="ECO:0007829|PDB:1BMV"
FT   HELIX           505..510
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          516..523
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          533..542
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   HELIX           550..553
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          554..561
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   TURN            563..565
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          567..573
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   HELIX           584..590
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          593..600
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          610..622
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          628..632
FT                   /evidence="ECO:0007829|PDB:1BMV"
FT   STRAND          635..648
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          650..652
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          657..661
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          667..669
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          672..674
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   HELIX           677..682
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          685..698
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          708..713
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   HELIX           724..726
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          727..732
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          740..745
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   HELIX           747..749
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          754..756
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   TURN            764..766
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          771..778
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          783..785
FT                   /evidence="ECO:0007829|PDB:1BMV"
FT   STRAND          788..805
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          829..835
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   TURN            842..844
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          846..853
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   TURN            854..857
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          858..861
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          863..865
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          868..871
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   HELIX           875..882
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          883..897
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          900..902
FT                   /evidence="ECO:0007829|PDB:1BMV"
FT   HELIX           904..906
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          910..917
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          921..923
FT                   /evidence="ECO:0007829|PDB:1BMV"
FT   STRAND          926..931
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          934..945
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   TURN            948..950
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   TURN            958..961
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          966..973
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   TURN            974..976
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          979..986
FT                   /evidence="ECO:0007829|PDB:1PGL"
FT   STRAND          991..997
FT                   /evidence="ECO:0007829|PDB:1PGL"
SQ   SEQUENCE   1018 AA;  113352 MW;  B11B35D0A7F0F872 CRC64;
     MFASFIFSGD NKLTEKTIFN CGDLDILVVY YTIATQFRKF LPHYIRWHLY TLLIYILPSF
     LTTEIKYKRN LSNIHISGLF YDNRFKFWTK HDKNLALTEE EKMEVIRNRG IPADVLAKRA
     HEFEKHVAHE SLKDQIPAVD KLYSTKVNKF AKIMNLRQSV VGDLKLLTDG KLYEGKHIPV
     SNISAGENHV VQIPLMAQEE ILSSSASDFK TAMVSKSSKP QATAMHVGAI EIIIDSFASP
     DCNIVGAMLL VDTYHTNPEN AVRSIFVAPF RGGRPIRVVT FPNTIVQIEP DMNSRFQLLS
     TTTNGDFVQG KDLAMVKVNV ACAAVGLTSS YTPTPLLESG LQKDRGLIVE YFGRMSYVAH
     NINQPQEKDL LEGNFSFDIK SRSRLEKVSS TKAQFVSGRT FKYDIIGAGS QSSEELSEEK
     IQGKAKQVDA RLRQRIDPQY NEVQAQMETN LFKLSLDDVE TPKGSMLDLK ISQSKIALPK
     NTVGGTILRS DLLANFLTEG NFRASVDLQR THRIKGMIKM VATVGIPENT GIALACAMNS
     SIRGRASSDI YTICSQDCEL WNPACTKAMT MSFNPNPCSD AWSLEFLKRT GFHCDIICVT
     GWTATPMQDV QVTIDWFISS QECVPRTYCV LNPQNPFVLN RWMGKLTFPQ GTSRSVKRMP
     LSIGGGAGAK SAILMNMPNA VLSMWRYFVG DLVFEVSKMT SPYIKCTVSF FIAFGNLADD
     TINFEAFPHK LVQFGEIQEK VVLKFSQEEF LTAWSTQVRP ATTLLADGCP YLYAMVHDSS
     VSTIPGDFVI GVKLTIIENM CAYGLNPGIS GSRLLGTIPQ SISQQTVWNQ MATVRTPLNF
     DSSKQSFCQF SVDLLGGGIS VDKTGDWITL VQNSPISNLL RVAAWKKGCL MVKVVMSGNA
     AVKRSDWASL VQVFLTNSNS TEHFDACRWT KSEPHSWELI FPIEVCGPNN GFEMWSSEWA
     NQTSWHLSFL VDNPKQSTTF DVLLGISQNF EIAGNTLMPA FSVPQANARS SENAESSA
//