ID CLF1_YEAST Reviewed; 687 AA. AC Q12309; D6VYB5; DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot. DT 01-NOV-1996, sequence version 1. DT 27-MAR-2024, entry version 173. DE RecName: Full=Pre-mRNA-splicing factor CLF1; DE AltName: Full=Crooked neck-like factor 1; DE AltName: Full=PRP19-associated complex protein 77; DE AltName: Full=Synthetic lethal with CDC40 protein 3; GN Name=CLF1; Synonyms=NTC77, SYF3; OrderedLocusNames=YLR117C; GN ORFNames=L2952; 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 [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 90840 / EAY235 / FY23; RX PubMed=9090053; RX DOI=10.1002/(sici)1097-0061(19970315)13:3<241::aid-yea61>3.0.co;2-#; RA Verhasselt P., Volckaert G.; RT "Sequence analysis of a 37.6 kbp cosmid clone from the right arm of RT Saccharomyces cerevisiae chromosome XII, carrying YAP3, HOG1, SNR6, tRNA- RT Arg3 and 23 new open reading frames, among which several homologies to RT proteins involved in cell division control and to mammalian growth factors RT and other animal proteins are found."; RL Yeast 13:241-250(1997). RN [2] 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 [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=9169871; RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J., RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., RA Zollner A., Hani J., Hoheisel J.D.; RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."; RL Nature 387:87-90(1997). RN [4] RP PROTEIN SEQUENCE OF 15-25, AND IDENTIFICATION IN THE PRP19-ASSOCIATED RP COMPLEX. RX PubMed=11842115; DOI=10.1093/nar/30.4.1029; RA Chen C.-H., Yu W.-C., Tsao T.Y., Wang L.-Y., Chen H.-R., Lin J.-Y., RA Tsai W.-Y., Cheng S.-C.; RT "Functional and physical interactions between components of the Prp19p- RT associated complex."; RL Nucleic Acids Res. 30:1029-1037(2002). RN [5] RP FUNCTION, AND INTERACTION WITH MUD2 AND PRP40. RX PubMed=10445879; DOI=10.1017/s1355838299990635; RA Chung S., McLean M.R., Rymond B.C.; RT "Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome RT assembly through stable U4/U6.U5 snRNP addition."; RL RNA 5:1042-1054(1999). RN [6] RP FUNCTION, AND INTERACTION WITH CEF1; ISY1; NTC20; PRP22 AND SYF2. RX PubMed=11102353; DOI=10.1093/genetics/156.4.1503; RA Ben-Yehuda S., Dix I., Russell C.S., McGarvey M., Beggs J.D., Kupiec M.; RT "Genetic and physical interactions between factors involved in both cell RT cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae."; RL Genetics 156:1503-1517(2000). RN [7] RP FUNCTION, AND IDENTIFICATION IN THE SPLICEOSOME. RX PubMed=11105756; DOI=10.1017/s1355838200000984; RA Russell C.S., Ben-Yehuda S., Dix I., Kupiec M., Beggs J.D.; RT "Functional analyses of interacting factors involved in both pre-mRNA RT splicing and cell cycle progression in Saccharomyces cerevisiae."; RL RNA 6:1565-1572(2000). RN [8] RP FUNCTION, AND INTERACTION WITH ORC2. RX PubMed=11973290; DOI=10.1093/genetics/160.4.1319; RA Zhu W., Rainville I.R., Ding M., Bolus M., Heintz N.H., Pederson D.S.; RT "Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA RT replication in Saccharomyces cerevisiae."; RL Genetics 160:1319-1333(2002). RN [9] RP IDENTIFICATION IN THE CWC COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY. RX PubMed=11884590; DOI=10.1128/mcb.22.7.2011-2024.2002; RA Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.; RT "Proteomics analysis reveals stable multiprotein complexes in both fission RT and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA RT splicing factors, and snRNAs."; RL Mol. Cell. Biol. 22:2011-2024(2002). RN [10] RP INTERACTION WITH ISY1; NTC20; PRP46 AND SYF1. RX PubMed=12088152; DOI=10.1017/s1355838202025050; RA Ohi M.D., Gould K.L.; RT "Characterization of interactions among the Cef1p-Prp19p-associated RT splicing complex."; RL RNA 8:798-815(2002). RN [11] RP FUNCTION, AND IDENTIFICATION IN THE SPLICEOSOME. RX PubMed=12509417; DOI=10.1074/jbc.m210839200; RA Wang Q., Hobbs K., Lynn B., Rymond B.C.; RT "The Clf1p splicing factor promotes spliceosome assembly through N-terminal RT tetratricopeptide repeat contacts."; RL J. Biol. Chem. 278:7875-7883(2003). RN [12] RP IDENTIFICATION BY MASS SPECTROMETRY. RX PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3; RA Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M., RA Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E., RA Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.; RT "Assigning function to yeast proteins by integration of technologies."; RL Mol. Cell 12:1353-1365(2003). RN [13] 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 [14] 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). CC -!- FUNCTION: Involved in pre-mRNA splicing and cell cycle progression. CC Required for the spliceosome assembly by promoting the functional CC integration of the U4/U6.U5 tri-snRNP particle into the U1-, U2- CC dependent pre-spliceosome. Also recruits PRP19 to the spliceosome, as a CC component of the NTC complex (or PRP19-associated complex). The CC association of the NTC complex to the spliceosome mediates CC conformational rearrangement or stabilizes the structure of the CC spliceosome after U4 snRNA dissociation, which leads to spliceosome CC maturation. Required for initiation of the DNA replication by binding CC the RNA replication origins, probably through its interaction with the CC origin recognition complex (ORC). {ECO:0000269|PubMed:10445879, CC ECO:0000269|PubMed:11102353, ECO:0000269|PubMed:11105756, CC ECO:0000269|PubMed:11973290, ECO:0000269|PubMed:12509417}. CC -!- SUBUNIT: Belongs to the NTC complex (or PRP19-associated complex), CC composed of at least CEF1, CLF1, ISY1, NTC20, SNT309, SYF1, SYF2, and CC PRP19. The NTC complex associates with the spliceosome after the CC release of the U1 and U4 snRNAs and forms the CWC spliceosome CC subcomplex (or CEF1-associated complex) reminiscent of a late-stage CC spliceosome composed also of the U2, U5 and U6 snRNAs and at least CC BUD13, BUD31, BRR2, CDC40, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23, CC CWC24, CWC25, CWC27, ECM2, HSH155, IST3, LEA1, MSL1, PRP8, PRP9, PRP11, CC PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, CC SNU114, SPP2, RSE1 and YJU2. Interacts with CEF1, ISY1, MUD2, NTC20, CC PRP22, PRP40, PRP46, SYF1, SYF2, and the ORC2 subunit of the origin CC recognition complex. {ECO:0000269|PubMed:10445879, CC ECO:0000269|PubMed:11102353, ECO:0000269|PubMed:11105756, CC ECO:0000269|PubMed:11842115, ECO:0000269|PubMed:11884590, CC ECO:0000269|PubMed:11973290, ECO:0000269|PubMed:12088152, CC ECO:0000269|PubMed:12509417}. CC -!- INTERACTION: CC Q12309; Q03654: CEF1; NbExp=8; IntAct=EBI-484, EBI-476; CC Q12309; P21374: ISY1; NbExp=4; IntAct=EBI-484, EBI-9382; CC Q12309; P38302: NTC20; NbExp=6; IntAct=EBI-484, EBI-20921; CC Q12309; P32523: PRP19; NbExp=9; IntAct=EBI-484, EBI-493; CC Q12309; Q06091: SNT309; NbExp=4; IntAct=EBI-484, EBI-818; CC Q12309; Q04048: SYF1; NbExp=4; IntAct=EBI-484, EBI-540; CC Q12309; P53277: SYF2; NbExp=2; IntAct=EBI-484, EBI-23308; CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}. CC -!- MISCELLANEOUS: Present with 2140 molecules/cell in log phase SD medium. CC {ECO:0000269|PubMed:14562106}. CC -!- SIMILARITY: Belongs to the crooked-neck family. {ECO:0000305}. 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; X89514; CAA61696.1; -; Genomic_DNA. DR EMBL; U53877; AAB82364.1; -; Genomic_DNA. DR EMBL; Z73289; CAA97685.1; -; Genomic_DNA. DR EMBL; BK006945; DAA09431.1; -; Genomic_DNA. DR PIR; S64954; S64954. DR RefSeq; NP_013218.1; NM_001182004.1. DR PDB; 5GM6; EM; 3.50 A; d=1-275. DR PDB; 5GMK; EM; 3.40 A; d=1-275. DR PDB; 5LJ3; EM; 3.80 A; S=1-687. DR PDB; 5LJ5; EM; 3.80 A; S=1-687. DR PDB; 5LQW; EM; 5.80 A; R=1-687. DR PDB; 5MPS; EM; 3.85 A; S=1-687. DR PDB; 5MQ0; EM; 4.17 A; S=1-687. DR PDB; 5WSG; EM; 4.00 A; d=36-275. DR PDB; 5Y88; EM; 3.70 A; I=1-687. DR PDB; 5YLZ; EM; 3.60 A; I=1-687. DR PDB; 6BK8; EM; 3.30 A; T=1-687. DR PDB; 6EXN; EM; 3.70 A; S=1-687. DR PDB; 6J6G; EM; 3.20 A; d=1-687. DR PDB; 6J6H; EM; 3.60 A; d=1-687. DR PDB; 6J6N; EM; 3.86 A; d=1-687. DR PDB; 6J6Q; EM; 3.70 A; d=1-687. DR PDBsum; 5GM6; -. DR PDBsum; 5GMK; -. DR PDBsum; 5LJ3; -. DR PDBsum; 5LJ5; -. DR PDBsum; 5LQW; -. DR PDBsum; 5MPS; -. DR PDBsum; 5MQ0; -. DR PDBsum; 5WSG; -. DR PDBsum; 5Y88; -. DR PDBsum; 5YLZ; -. DR PDBsum; 6BK8; -. DR PDBsum; 6EXN; -. DR PDBsum; 6J6G; -. DR PDBsum; 6J6H; -. DR PDBsum; 6J6N; -. DR PDBsum; 6J6Q; -. DR AlphaFoldDB; Q12309; -. DR SMR; Q12309; -. DR BioGRID; 31389; 290. DR ComplexPortal; CPX-1651; PRP19-associated complex. DR ComplexPortal; CPX-1885; NineTeen complex. DR DIP; DIP-1685N; -. DR IntAct; Q12309; 36. DR MINT; Q12309; -. DR STRING; 4932.YLR117C; -. DR MoonProt; Q12309; -. DR MaxQB; Q12309; -. DR PaxDb; 4932-YLR117C; -. DR PeptideAtlas; Q12309; -. DR EnsemblFungi; YLR117C_mRNA; YLR117C; YLR117C. DR GeneID; 850808; -. DR KEGG; sce:YLR117C; -. DR AGR; SGD:S000004107; -. DR SGD; S000004107; CLF1. DR VEuPathDB; FungiDB:YLR117C; -. DR eggNOG; KOG1915; Eukaryota. DR GeneTree; ENSGT00550000074931; -. DR HOGENOM; CLU_011554_1_0_1; -. DR InParanoid; Q12309; -. DR OMA; HIKVWIS; -. DR OrthoDB; 5479069at2759; -. DR BioCyc; YEAST:G3O-32262-MONOMER; -. DR BioGRID-ORCS; 850808; 0 hits in 10 CRISPR screens. DR PRO; PR:Q12309; -. DR Proteomes; UP000002311; Chromosome XII. DR RNAct; Q12309; Protein. DR GO; GO:0000785; C:chromatin; IDA:SGD. DR GO; GO:0071014; C:post-mRNA release spliceosomal complex; IBA:GO_Central. DR GO; GO:0000974; C:Prp19 complex; IDA:SGD. DR GO; GO:0071006; C:U2-type catalytic step 1 spliceosome; IDA:SGD. DR GO; GO:0071007; C:U2-type catalytic step 2 spliceosome; IDA:SGD. DR GO; GO:0071008; C:U2-type post-mRNA release spliceosomal complex; IDA:SGD. DR GO; GO:0071004; C:U2-type prespliceosome; IDA:SGD. DR GO; GO:0003682; F:chromatin binding; IDA:SGD. DR GO; GO:0003688; F:DNA replication origin binding; IDA:SGD. DR GO; GO:0000354; P:cis assembly of pre-catalytic spliceosome; IMP:SGD. DR GO; GO:0006270; P:DNA replication initiation; IMP:SGD. DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central. DR GO; GO:0000245; P:spliceosomal complex assembly; IBA:GO_Central. DR Gene3D; 1.25.40.10; Tetratricopeptide repeat domain; 2. DR InterPro; IPR003107; HAT. DR InterPro; IPR045075; Syf1-like. DR InterPro; IPR011990; TPR-like_helical_dom_sf. DR PANTHER; PTHR11246:SF3; CROOKED NECK-LIKE PROTEIN 1; 1. DR PANTHER; PTHR11246; PRE-MRNA SPLICING FACTOR; 1. DR Pfam; PF02184; HAT; 1. DR SMART; SM00386; HAT; 12. DR SUPFAM; SSF48452; TPR-like; 2. PE 1: Evidence at protein level; KW 3D-structure; Direct protein sequencing; mRNA processing; mRNA splicing; KW Nucleus; Reference proteome; Repeat; Spliceosome. FT CHAIN 1..687 FT /note="Pre-mRNA-splicing factor CLF1" FT /id="PRO_0000205753" FT REPEAT 45..77 FT /note="HAT 1" FT REPEAT 79..111 FT /note="HAT 2" FT REPEAT 113..145 FT /note="HAT 3" FT REPEAT 147..178 FT /note="HAT 4" FT REPEAT 180..211 FT /note="HAT 5" FT REPEAT 213..247 FT /note="HAT 6" FT REPEAT 251..283 FT /note="HAT 7" FT REPEAT 300..332 FT /note="HAT 8" FT REPEAT 337..369 FT /note="HAT 9" FT REPEAT 383..416 FT /note="HAT 10" FT REPEAT 451..483 FT /note="HAT 11" FT REPEAT 525..557 FT /note="HAT 12" FT REPEAT 629..661 FT /note="HAT 13" FT HELIX 15..27 FT /evidence="ECO:0007829|PDB:6BK8" FT HELIX 40..60 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 65..77 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 81..94 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 99..111 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 115..128 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 133..145 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 149..159 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 166..179 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 182..195 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 199..212 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 215..231 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 232..234 FT /evidence="ECO:0007829|PDB:6BK8" FT HELIX 240..256 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 260..273 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 278..291 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 294..315 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 320..333 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 337..349 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 354..369 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 375..382 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 383..385 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 389..395 FT /evidence="ECO:0007829|PDB:6J6G" FT STRAND 398..400 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 406..417 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 425..438 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 447..459 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 463..474 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 481..493 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 498..511 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 515..522 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 532..547 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 557..570 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 576..589 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 597..614 FT /evidence="ECO:0007829|PDB:6J6G" FT HELIX 621..635 FT /evidence="ECO:0007829|PDB:6J6G" SQ SEQUENCE 687 AA; 82445 MW; AE7D5EC5B3979E00 CRC64; MDTLEPTAVD THVSAEQILR DVYKKGQKAR GSTNIDILDL EELREYQRRK RTEYEGYLKR NRLDMGQWIR YAQFEIEQHD MRRARSIFER ALLVDSSFIP LWIRYIDAEL KVKCINHARN LMNRAISTLP RVDKLWYKYL IVEESLNNVE IVRSLYTKWC SLEPGVNAWN SFVDFEIRQK NWNGVREIYS KYVMAHPQMQ TWLKWVRFEN RHGNTEFTRS VYSLAIDTVA NLQNLQIWSD MEVAKLVNSF AHWEAAQQEY ERSSALYQIA IEKWPSNQLL KAGLLDFEKQ FGDINSIEET ISYKRKMEYE TILSNNAYDY DTWWLYLDLI SESFPKQIMQ TFEKAIVDSR PKELSKNVQW KRYIYLWMRY ICYVELELEN SLLEEELFQR LIDDIIPHKH FTFSKIWLMY AKFLIRHDDV PKARKILGKA IGLCPKAKTF KGYIELEVKL KEFDRVRKIY EKFIEFQPSD LQIWSQYGEL EENLGDWDRV RGIYTIALDE NSDFLTKEAK IVLLQKYITF ETESQEFEKA RKLYRRYLEL NQYSPQSWIE FAMYQTSTPT EQQLLDLAKL QSENVDEDIE FEITDENKLE ARKVFEEAIV FFKEKDDKQG RLSILEALKD YEETYGTELD QETVKKRFPK VIKKVRLQNG VEEEFVDYIF PDDIDDDKPK PSKFLELAKK WKQEQAL //