ID   RAF1_ORYSJ              Reviewed;         469 AA.
AC   Q7XDY9; A0A0P0XV97;
DT   13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2003, sequence version 1.
DT   03-AUG-2022, entry version 101.
DE   RecName: Full=Rubisco accumulation factor 1, chloroplastic;
DE   Flags: Precursor;
GN   Name=RAF1; OrderedLocusNames=Os10g0445600, LOC_Os10g30870;
GN   ORFNames=OsJ_31693;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12791992; DOI=10.1126/science.1083523;
RA   Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA   Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA   Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA   Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA   Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA   Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA   Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA   Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA   Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA   Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA   Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA   Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA   Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA   Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA   Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA   Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA   Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT   "In-depth view of structure, activity, and evolution of rice chromosome
RT   10.";
RL   Science 300:1566-1569(2003).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
RN   [7]
RP   IDENTIFICATION.
RX   PubMed=22942379; DOI=10.1105/tpc.112.102012;
RA   Feiz L., Williams-Carrier R., Wostrikoff K., Belcher S., Barkan A.,
RA   Stern D.B.;
RT   "Ribulose-1,5-bis-phosphate carboxylase/oxygenase accumulation factor1 is
RT   required for holoenzyme assembly in maize.";
RL   Plant Cell 24:3435-3446(2012).
CC   -!- FUNCTION: Required for assembly or stability of RuBisCO. Acts at a
CC       postchaperonin step to fold and/or assemble the large subunit (LS) into
CC       RuBisCO (By similarity). {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC   -!- DOMAIN: Has 3 domains, the N-terminal alpha-helical domain, an extended
CC       flexible linker and the C-terminal beta-sheet domain. The N-terminal
CC       alpha-helical domain stabilizes RbcL dimers and RbcL dimer-dimer
CC       interactions, facilitating RbcL(8) formation. The C-terminal beta-sheet
CC       domain probably dimerizes Raf1 (By similarity). The 2 C-terminal beta-
CC       sheet domains are swapped and pack against each other to form the dimer
CC       interface (By similarity). {ECO:0000250|UniProtKB:Q8YLP6,
CC       ECO:0000250|UniProtKB:Q9SR19}.
CC   -!- SIMILARITY: Belongs to the RAF family. {ECO:0000305}.
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DR   EMBL; DP000086; AAP54002.1; -; Genomic_DNA.
DR   EMBL; AP008216; BAF26626.1; -; Genomic_DNA.
DR   EMBL; AP014966; BAT11069.1; -; Genomic_DNA.
DR   EMBL; CM000147; EAZ16239.1; -; Genomic_DNA.
DR   EMBL; AK120673; BAH00120.1; -; mRNA.
DR   RefSeq; XP_015614647.1; XM_015759161.1.
DR   AlphaFoldDB; Q7XDY9; -.
DR   SMR; Q7XDY9; -.
DR   STRING; 4530.OS10T0445600-01; -.
DR   PaxDb; Q7XDY9; -.
DR   PRIDE; Q7XDY9; -.
DR   EnsemblPlants; Os10t0445600-01; Os10t0445600-01; Os10g0445600.
DR   GeneID; 4348745; -.
DR   Gramene; Os10t0445600-01; Os10t0445600-01; Os10g0445600.
DR   KEGG; osa:4348745; -.
DR   eggNOG; ENOG502QRYH; Eukaryota.
DR   HOGENOM; CLU_041979_0_0_1; -.
DR   InParanoid; Q7XDY9; -.
DR   OMA; IVASQVY; -.
DR   OrthoDB; 1337198at2759; -.
DR   Proteomes; UP000000763; Chromosome 10.
DR   Proteomes; UP000007752; Chromosome 10.
DR   Proteomes; UP000059680; Chromosome 10.
DR   Genevisible; Q7XDY9; OS.
DR   GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR   GO; GO:0110102; P:ribulose bisphosphate carboxylase complex assembly; IEA:UniProt.
DR   InterPro; IPR037494; RAF1.
DR   InterPro; IPR040858; Raf1_C.
DR   InterPro; IPR040781; Raf1_HTH.
DR   InterPro; IPR041358; Raf1_N.
DR   PANTHER; PTHR35299; PTHR35299; 1.
DR   Pfam; PF18579; Raf1_HTH; 1.
DR   Pfam; PF18578; Raf1_N; 1.
DR   Pfam; PF18087; RuBisCo_chap_C; 1.
PE   2: Evidence at transcript level;
KW   Chaperone; Chloroplast; Coiled coil; Plastid; Reference proteome;
KW   Transit peptide.
FT   TRANSIT         1..46
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255"
FT   CHAIN           47..469
FT                   /note="Rubisco accumulation factor 1, chloroplastic"
FT                   /id="PRO_0000424241"
FT   REGION          1..78
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          90..281
FT                   /note="N-terminal alpha-helix"
FT                   /evidence="ECO:0000250|UniProtKB:Q9SR19"
FT   REGION          311..456
FT                   /note="C-terminal beta sheet"
FT                   /evidence="ECO:0000250|UniProtKB:Q9SR19"
FT   COILED          246..294
FT                   /evidence="ECO:0000255"
FT   COMPBIAS        19..42
FT                   /note="Basic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   469 AA;  51560 MW;  D6FDA08B4960EC24 CRC64;
     MLSLSHPHPH PASTTAAAAA RHHHRRNAPF APHHRRRRRF AHLTTSAVIL GPDGRPIGGG
     PRDNKLPFTP PPTAPPDQLY QPFHPPPSPL PDKYKDLDLG QRLAVLRDRL GLWHEYAPLI
     SALSREGFTP SSIEEATGIS GVEQNSVVVA TQVRDSLVAD EGGFPAELLR YFDSYGGPEL
     LYELRFLNAR QRADAARHAI DRRLEPRGVR ELARSMKDFP QRRGDDGWEA FTRDNPGDCL
     AFARFRQSRE AIDAEDSVAE LERALEVVDT EPARARVEAE LDRARRKAAG EEVDDEDGAA
     NAAAAASRPA VPVVRLMYGE VAEATTVLLL PVVREGDGGE ALAHAPRRTR TDADLGMVEV
     DKGWTRWAVV PGWGPVAEVA GEAVVIELAD GRTLPWRSAE AERVLVVANR GRREVVEDGI
     YVVEREGRLV VEKGRKLAAE GVGEAAAEVL VVVRPPRDED DMISDDEWD