ID   CLU_YEAST               Reviewed;        1277 AA.
AC   Q03690; D6VZI6;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 1.
DT   02-SEP-2026, entry version 186.
DE   RecName: Full=Clustered mitochondria protein 1;
DE   AltName: Full=Translation initiation factor 31;
DE   AltName: Full=eIF3-associated protein p135;
GN   Name=CLU1 {ECO:0000255|HAMAP-Rule:MF_03013};
GN   Synonyms=TIF31 {ECO:0000255|HAMAP-Rule:MF_03013};
GN   OrderedLocusNames=YMR012W; ORFNames=YM8270.16;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, AND
RP   ASSOCIATION WITH THE EIF-3 COMPLEX.
RC   STRAIN=ATCC 204511 / S288c / AB972;
RX   PubMed=10358023; DOI=10.1074/jbc.274.24.16802;
RA   Vornlocher H.-P., Hanachi P., Ribeiro S., Hershey J.W.B.;
RT   "A 110-kilodalton subunit of translation initiation factor eIF3 and an
RT   associated 135-kilodalton protein are encoded by the Saccharomyces
RT   cerevisiae TIF32 and TIF31 genes.";
RL   J. Biol. Chem. 274:16802-16812(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169872; DOI=10.1038/387s090;
RA   Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA   Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA   Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA   Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL   Nature 387:90-93(1997).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [4]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=9601101; DOI=10.1242/jcs.111.12.1717;
RA   Fields S.D., Conrad M.N., Clarke M.;
RT   "The S. cerevisiae CLU1 and D. discoideum cluA genes are functional
RT   homologues that influence mitochondrial morphology and distribution.";
RL   J. Cell Sci. 111:1717-1727(1998).
RN   [5]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [6]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
RN   [7]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND ASSOCIATION WITH THE 80S RIBOSOME.
RX   PubMed=16215987; DOI=10.1002/jcb.20658;
RA   Jao D.L., Chen K.Y.;
RT   "Tandem affinity purification revealed the hypusine-dependent binding of
RT   eukaryotic initiation factor 5A to the translating 80S ribosomal complex.";
RL   J. Cell. Biochem. 97:583-598(2006).
RN   [8]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1247, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT   "A multidimensional chromatography technology for in-depth phosphoproteome
RT   analysis.";
RL   Mol. Cell. Proteomics 7:1389-1396(2008).
RN   [9]
RP   INDUCTION.
RX   PubMed=19804647; DOI=10.1186/1471-2164-10-461;
RA   Rintala E., Toivari M., Pitkanen J.P., Wiebe M.G., Ruohonen L.,
RA   Penttila M.;
RT   "Low oxygen levels as a trigger for enhancement of respiratory metabolism
RT   in Saccharomyces cerevisiae.";
RL   BMC Genomics 10:461-461(2009).
RN   [10]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1247, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19779198; DOI=10.1126/science.1172867;
RA   Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT   "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT   into evolution.";
RL   Science 325:1682-1686(2009).
CC   -!- FUNCTION: mRNA-binding protein involved in proper cytoplasmic
CC       distribution of mitochondria. {ECO:0000255|HAMAP-Rule:MF_03013,
CC       ECO:0000269|PubMed:9601101}.
CC   -!- SUBUNIT: May associate with the eukaryotic translation initiation
CC       factor 3 (eIF-3) complex. Associates with the 80S ribosome.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_03013,
CC       ECO:0000269|PubMed:14562095}.
CC   -!- INDUCTION: Expression is increased in intermediate compared to fully
CC       aerobic conditions. {ECO:0000269|PubMed:19804647}.
CC   -!- DISRUPTION PHENOTYPE: Causes mitochondria to cluster within cells.
CC       {ECO:0000269|PubMed:9601101}.
CC   -!- MISCELLANEOUS: Present with 17000 molecules/cell in log phase SD
CC       medium. {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the CLU family. {ECO:0000255|HAMAP-
CC       Rule:MF_03013}.
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DR   EMBL; AF004911; AAB82415.1; -; Genomic_DNA.
DR   EMBL; Z48613; CAA88529.1; -; Genomic_DNA.
DR   EMBL; BK006946; DAA09910.1; -; Genomic_DNA.
DR   PIR; S53043; S53043.
DR   RefSeq; NP_013725.1; NM_001182508.1.
DR   AlphaFoldDB; Q03690; -.
DR   SMR; Q03690; -.
DR   BioGRID; 35182; 236.
DR   DIP; DIP-5924N; -.
DR   FunCoup; Q03690; 1287.
DR   IntAct; Q03690; 100.
DR   MINT; Q03690; -.
DR   STRING; 4932.YMR012W; -.
DR   iPTMnet; Q03690; -.
DR   PaxDb; 4932-YMR012W; -.
DR   PeptideAtlas; Q03690; -.
DR   EnsemblFungi; YMR012W_mRNA; YMR012W; YMR012W.
DR   GeneID; 855025; -.
DR   KEGG; sce:YMR012W; -.
DR   AGR; SGD:S000004614; -.
DR   SGD; S000004614; CLU1.
DR   VEuPathDB; FungiDB:YMR012W; -.
DR   eggNOG; KOG1839; Eukaryota.
DR   HOGENOM; CLU_003256_2_0_1; -.
DR   InParanoid; Q03690; -.
DR   OMA; HPVWDKD; -.
DR   OrthoDB; 1414216at2759; -.
DR   BioCyc; YEAST:G3O-32720-MONOMER; -.
DR   BioGRID-ORCS; 855025; 2 hits in 10 CRISPR screens.
DR   CD-CODE; 67785C55; Hypersomatic shock foci.
DR   CD-CODE; E03F929F; Stress granule.
DR   PRO; PR:Q03690; -.
DR   Proteomes; UP000002311; Chromosome XIII.
DR   RNAct; Q03690; protein.
DR   GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR   GO; GO:0036464; C:cytoplasmic ribonucleoprotein granule; IDA:SGD.
DR   GO; GO:0010494; C:cytoplasmic stress granule; HDA:SGD.
DR   GO; GO:0003729; F:mRNA binding; HDA:SGD.
DR   GO; GO:0003723; F:RNA binding; IDA:SGD.
DR   GO; GO:0048312; P:intracellular distribution of mitochondria; IBA:GO_Central.
DR   GO; GO:0007005; P:mitochondrion organization; IEA:UniProtKB-UniRule.
DR   GO; GO:2000765; P:regulation of cytoplasmic translation; IMP:SGD.
DR   CDD; cd15466; CLU-central; 1.
DR   CDD; cd22249; UDM1_RNF168_RNF169-like; 1.
DR   FunFam; 1.25.40.10:FF:001563; Clustered mitochondria protein homolog; 1.
DR   Gene3D; 1.25.40.10; Tetratricopeptide repeat domain; 1.
DR   HAMAP; MF_03013; CLU; 1.
DR   InterPro; IPR033646; CLU-central.
DR   InterPro; IPR025697; CLU_dom.
DR   InterPro; IPR028275; CLU_N.
DR   InterPro; IPR027523; CLU_prot.
DR   InterPro; IPR023231; GSKIP_dom_sf.
DR   InterPro; IPR011990; TPR-like_helical_dom_sf.
DR   PANTHER; PTHR12601:SF6; CLUSTERED MITOCHONDRIA PROTEIN HOMOLOG; 1.
DR   PANTHER; PTHR12601; EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT EIF-3; 1.
DR   Pfam; PF13236; CLU; 1.
DR   Pfam; PF15044; CLU_N; 1.
DR   Pfam; PF12807; eIF3_p135; 1.
DR   Pfam; PF13374; TPR_10; 1.
DR   SUPFAM; SSF103107; Hypothetical protein c14orf129, hspc210; 1.
DR   SUPFAM; SSF48452; TPR-like; 1.
DR   PROSITE; PS51823; CLU; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; Direct protein sequencing; Phosphoprotein; Reference proteome;
KW   Repeat; TPR repeat.
FT   CHAIN           1..1277
FT                   /note="Clustered mitochondria protein 1"
FT                   /id="PRO_0000123557"
FT   DOMAIN          339..596
FT                   /note="Clu"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01167"
FT   REPEAT          704..738
FT                   /note="TPR 1"
FT   REPEAT          1020..1053
FT                   /note="TPR 2"
FT   REPEAT          1148..1181
FT                   /note="TPR 3"
FT   REGION          19..39
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          148..176
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1212..1277
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        27..36
FT                   /note="Basic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        153..176
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1235..1249
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1264..1277
FT                   /note="Basic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         1247
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956,
FT                   ECO:0007744|PubMed:19779198"
SQ   SEQUENCE   1277 AA;  145166 MW;  1E643F4EE77ED5B5 CRC64;
     MSEKKEEVKN ATVKVTVKLP KEDNHSHNTK HLKKTQSSKN NDISFEIGKE SKIQTVLDVL
     AMIPSSKYLT NVGLKTIEGD SQLSDEMSIK EIVGEKSELK LQLILKPYSA REALKHVITV
     RDFIGFAQET SDGLSEFAIS TGSSFSSLPL GPIKERSKQE EKDEKSDPEE KKNTFKDVTD
     EEKLKFNEMV HEVFSSFKNS SINKLLTSES NIITPCVRSL SFAPYNPVPP FYRSKGHLFY
     LQIVTLEGES FYITAIPSGF YVNKSNSTKF DPSPKENTDE NAHSSLIYYS LFDLIASRSK
     KFISHVQAFE KKLSALDSTS YVRPSNTFLH KPWFVSSLPP NNPDYLRLQT AALDTTPERN
     FNDEFQAIKD LTTSTLQDRI EMERLFSKVV HEFSVTAASG AMSIFYSDFV AMNPESPTRD
     QIFLKDNIFY SYVSDVSGNY EGKGGDEAAI AASNQDLKTI NILNRLHMHE VRYLLTTVVE
     FAGRRILAQT PVPGLLATMG NKIVKDANTG EEVTEDFVND INVKYGLDEG LGKIVYDADF
     DSVLEKKFVK AFHLKKHKVN GTELAFSSQS KGIVGFDKRR YILDLANTYP LDINFARQNF
     DNIEETGNRY PHRQTLLRPE LVEKWWNNKV EKEGVEFEKA YEENLFSYNP DAYQVEGIED
     ANVDEMSNYL QKEVIPSVIQ DYLSGNLSTP YNGEHLADTL HKNGINMRYL GKIIELSQKE
     LDSQIVHYEQ NLKAVEQDNK EYEDWEKSYL QKIENMIKER QAKINKLVQE GKEVPKELTE
     DLKLNDEEIK KPTDGKPVVV AYDELVPLIK ISELEIVSRS LKHVLKDLSK DVPVFLVPSL
     VAYVFNMLVG INYNADPKPE PVDEFYPVNK CSFAKLTRSE LLEAVSKQAF LRFRHQLPSN
     WIEAYMENPF TLIRSVSYKF GIQLLNKEYF FTREQLESYK QSLDKKIRNK FVEPPTTFSL
     SDLTIIPRVK FSEYTSSVSE EFWAQGASMI NEDKQSALTL LAQSITVLED VNNILHPAVA
     EKYLSLSAIY NKLALYPEAI AFCRKACTIY ERVSGIDSFE MMRALTNLAI LEFSNESPYN
     ATVVYNRLAE ILKVYELPKI HHPAPTSIFN HLEQLALGVQ DTKLAIEVLG QLSSYVVELE
     GKDSLAYGYT ESRLGNLFAA LKDFHRALEH ITVTQGIFTK QLGMNHTHSA QSRQWVNGLS
     SLIMDLKQKK QLAQDQMSTT GSNSAGHKKT NHRQKKDDVK PELANKSVDE LLTFIEGDSS
     NSKSKNKTNN KKKHGKK
//