ID   IPI3_YEAST              Reviewed;         555 AA.
AC   P53877; D6W104;
DT   01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1996, sequence version 1.
DT   02-SEP-2026, entry version 187.
DE   RecName: Full=Pre-rRNA-processing protein IPI3;
DE   AltName: Full=Involved in processing IST2 protein 3;
GN   Name=IPI3; OrderedLocusNames=YNL182C; ORFNames=N1636;
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 204508 / S288c;
RX   PubMed=9169873; DOI=10.1038/387s093;
RA   Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA   Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA   Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA   Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA   Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA   Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA   Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA   Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA   Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA   Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA   Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA   Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA   Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA   Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA   Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA   Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA   Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT   evolutionary implications.";
RL   Nature 387:93-98(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   IDENTIFICATION IN THE RIX1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY,
RP   AND INTERACTION WITH RIX1.
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   [4]
RP   IDENTIFICATION IN THE RIX1 COMPLEX, SUBCELLULAR LOCATION, FUNCTION OF THE
RP   RIX1 COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX   PubMed=15528184; DOI=10.1074/jbc.m406876200;
RA   Galani K., Nissan T.A., Petfalski E., Tollervey D., Hurt E.;
RT   "Rea1, a dynein-related nuclear AAA-ATPase, is involved in late rRNA
RT   processing and nuclear export of 60 S subunits.";
RL   J. Biol. Chem. 279:55411-55418(2004).
RN   [5]
RP   IDENTIFICATION IN THE RIX1 COMPLEX, AND FUNCTION OF THE RIX1 COMPLEX.
RX   PubMed=14759368; DOI=10.1016/s1097-2765(04)00003-6;
RA   Krogan N.J., Peng W.-T., Cagney G., Robinson M.D., Haw R., Zhong G.,
RA   Guo X., Zhang X., Canadien V., Richards D.P., Beattie B.K., Lalev A.,
RA   Zhang W., Davierwala A.P., Mnaimneh S., Starostine A., Tikuisis A.P.,
RA   Grigull J., Datta N., Bray J.E., Hughes T.R., Emili A., Greenblatt J.F.;
RT   "High-definition macromolecular composition of yeast RNA-processing
RT   complexes.";
RL   Mol. Cell 13:225-239(2004).
RN   [6]
RP   IDENTIFICATION IN THE RIX1 COMPLEX, INTERACTION WITH MDN1 AND PRE-60S
RP   RIBOSOMAL PARTICLES, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX   PubMed=15260980; DOI=10.1016/j.molcel.2004.06.033;
RA   Nissan T.A., Galani K., Maco B., Tollervey D., Aebi U., Hurt E.;
RT   "A pre-ribosome with a tadpole-like structure functions in ATP-dependent
RT   maturation of 60S subunits.";
RL   Mol. Cell 15:295-301(2004).
RN   [7]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-388, 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   [8]
RP   IDENTIFICATION IN THE RIX1 COMPLEX.
RX   PubMed=26619264; DOI=10.1038/nsmb.3132;
RA   Barrio-Garcia C., Thoms M., Flemming D., Kater L., Berninghausen O.,
RA   Bassler J., Beckmann R., Hurt E.;
RT   "Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome
RT   remodeling.";
RL   Nat. Struct. Mol. Biol. 23:37-44(2016).
CC   -!- FUNCTION: Component of the RIX1 complex required for processing of ITS2
CC       sequences from 35S pre-rRNA. {ECO:0000269|PubMed:14759368,
CC       ECO:0000269|PubMed:15528184}.
CC   -!- SUBUNIT: Component of the RIX1 complex, composed of IPI1, RIX1/IPI2 and
CC       IPI3 in a 1:2:2 stoichiometry. The complex interacts (via RIX1) with
CC       MDN1 (via its hexameric AAA ATPase ring) and the pre-60S ribosome
CC       particles. Interacts with RIX1. {ECO:0000269|PubMed:14690591,
CC       ECO:0000269|PubMed:14759368, ECO:0000269|PubMed:15260980,
CC       ECO:0000269|PubMed:15528184}.
CC   -!- INTERACTION:
CC       P53877; P38883: RIX1; NbExp=9; IntAct=EBI-29063, EBI-24899;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15528184}.
CC   -!- DOMAIN: The coiled-coil motif forms a homodimeric contact and
CC       facilitates RIX1 complex oligomerization.
CC       {ECO:0000305|PubMed:26619264}.
CC   -!- SIMILARITY: Belongs to the WD repeat IPI3/WDR18 family. {ECO:0000305}.
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DR   EMBL; Z71458; CAA96075.1; -; Genomic_DNA.
DR   EMBL; BK006947; DAA10370.1; -; Genomic_DNA.
DR   PIR; S63137; S63137.
DR   RefSeq; NP_014217.1; NM_001183020.1.
DR   PDB; 6YLE; EM; 3.30 A; A/B=1-555.
DR   PDB; 6YLH; EM; 3.10 A; 0/w=1-555.
DR   AlphaFoldDB; P53877; -.
DR   EMDB; EMD-10836; -.
DR   EMDB; EMD-10839; -.
DR   SMR; P53877; -.
DR   BioGRID; 35650; 160.
DR   ComplexPortal; CPX-1711; RIX1 complex.
DR   DIP; DIP-4297N; -.
DR   FunCoup; P53877; 537.
DR   IntAct; P53877; 57.
DR   MINT; P53877; -.
DR   STRING; 4932.YNL182C; -.
DR   iPTMnet; P53877; -.
DR   PaxDb; 4932-YNL182C; -.
DR   PeptideAtlas; P53877; -.
DR   EnsemblFungi; YNL182C_mRNA; YNL182C; YNL182C.
DR   GeneID; 855539; -.
DR   KEGG; sce:YNL182C; -.
DR   AGR; SGD:S000005126; -.
DR   SGD; S000005126; IPI3.
DR   VEuPathDB; FungiDB:YNL182C; -.
DR   eggNOG; KOG0646; Eukaryota.
DR   HOGENOM; CLU_029749_4_0_1; -.
DR   InParanoid; P53877; -.
DR   OMA; WEAHYNK; -.
DR   OrthoDB; 756370at2759; -.
DR   BioCyc; YEAST:G3O-33193-MONOMER; -.
DR   Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR   BioGRID-ORCS; 855539; 3 hits in 10 CRISPR screens.
DR   PRO; PR:P53877; -.
DR   Proteomes; UP000002311; Chromosome XIV.
DR   RNAct; P53877; protein.
DR   GO; GO:0005656; C:nuclear pre-replicative complex; IDA:SGD.
DR   GO; GO:0005654; C:nucleoplasm; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; HDA:SGD.
DR   GO; GO:0120330; C:rixosome complex; IDA:SGD.
DR   GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR   GO; GO:0006261; P:DNA-templated DNA replication; IBA:GO_Central.
DR   GO; GO:0006267; P:pre-replicative complex assembly involved in nuclear cell cycle DNA replication; IMP:SGD.
DR   GO; GO:0030174; P:regulation of DNA-templated DNA replication initiation; IMP:SGD.
DR   GO; GO:0000027; P:ribosomal large subunit assembly; IMP:SGD.
DR   GO; GO:0006364; P:rRNA processing; IMP:SGD.
DR   FunFam; 2.130.10.10:FF:001736; Pre-rRNA-processing protein IPI3; 1.
DR   Gene3D; 2.130.10.10; YVTN repeat-like/Quinoprotein amine dehydrogenase; 1.
DR   InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR   InterPro; IPR036322; WD40_repeat_dom_sf.
DR   InterPro; IPR001680; WD40_rpt.
DR   InterPro; IPR045227; WDR18/Ipi3/RID3.
DR   PANTHER; PTHR18763:SF0; WD REPEAT-CONTAINING PROTEIN 18; 1.
DR   PANTHER; PTHR18763; WD-REPEAT PROTEIN 18; 1.
DR   Pfam; PF00400; WD40; 2.
DR   SMART; SM00320; WD40; 3.
DR   SUPFAM; SSF50978; WD40 repeat-like; 1.
DR   PROSITE; PS50082; WD_REPEATS_2; 1.
DR   PROSITE; PS50294; WD_REPEATS_REGION; 1.
DR   PDBsum; 6YLE; -.
DR   PDBsum; 6YLH; -.
PE   1: Evidence at protein level;
KW   3D-structure; Coiled coil; Nucleus; Phosphoprotein; Reference proteome;
KW   Repeat; Ribosome biogenesis; rRNA processing; WD repeat.
FT   CHAIN           1..555
FT                   /note="Pre-rRNA-processing protein IPI3"
FT                   /id="PRO_0000051484"
FT   REPEAT          29..68
FT                   /note="WD 1"
FT                   /evidence="ECO:0000255"
FT   REPEAT          90..133
FT                   /note="WD 2"
FT                   /evidence="ECO:0000255"
FT   REPEAT          137..176
FT                   /note="WD 3"
FT                   /evidence="ECO:0000255"
FT   REPEAT          187..234
FT                   /note="WD 4"
FT                   /evidence="ECO:0000255"
FT   REPEAT          255..296
FT                   /note="WD 5"
FT                   /evidence="ECO:0000255"
FT   REPEAT          342..383
FT                   /note="WD 6"
FT                   /evidence="ECO:0000255"
FT   REGION          460..504
FT                   /note="Interaction with RIX1"
FT                   /evidence="ECO:0000269|PubMed:26619264"
FT   COILED          513..554
FT                   /evidence="ECO:0000255"
FT   MOD_RES         388
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   STRAND          4..11
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          13..19
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          23..28
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          37..40
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   TURN            41..43
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          44..48
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   TURN            50..52
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          53..59
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          62..64
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          71..74
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          81..85
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   TURN            94..96
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   HELIX           101..103
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          109..114
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   HELIX           116..118
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          120..124
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   TURN            125..128
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          129..135
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          137..140
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          142..158
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          163..168
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   HELIX           169..171
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          182..185
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          192..198
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          208..216
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   TURN            217..219
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          220..228
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          249..255
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          260..265
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          271..278
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          280..288
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          294..297
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          311..315
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          335..338
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          347..352
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          359..363
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          366..372
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   TURN            373..376
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          377..383
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          395..401
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   HELIX           433..435
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          437..439
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   STRAND          450..453
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   HELIX           459..461
FT                   /evidence="ECO:0007829|PDB:6YLH"
FT   HELIX           473..484
FT                   /evidence="ECO:0007829|PDB:6YLH"
SQ   SEQUENCE   555 AA;  61773 MW;  8EED6854DF9405A6 CRC64;
     MDEQVIFTTN TSGTIASVHS FEQINLRQCS TQSRNSCVQV GNKYLFIAQA QKALINVYNL
     SGSFKRESVE QRLPLPEILK CLEVVENDGV QYDRIQGVNH NLPDFNLPYL LLGSTESGKL
     YIWELNSGIL LNVKPMAHYQ SITKIKSILN GKYIITSGND SRVIIWQTVD LVSASNDDPK
     PLCILHDHTL PVTDFQVSSS QGKFLSCTDT KLFTVSQDAT IRCYDLSLIG SKKKQKANEN
     DVSIGKTPVL LATFTTPYSI KSIVLDPADR ACYIGTAEGC FSLNLFYKLK GNAIVNLLQS
     AGVNTVQKGR VFSLVQRNSL TGGENEDLDA LYAMGQLVCE NVLNSNVSCL EISMDGTLLL
     IGDTEGKVSI AEIYSKQIIR TIQTLTTSQD SVGEVTNLLT NPYRLERGNL LFEGESKGKQ
     PSNNNGHNFM KIPNLQRVIF DGKNKGHLHD IWYQIGEPEA ETDPNLALPL NDFNAYLEQV
     KTQESIFSHI GKVSSNVKVI DNKIDATSSL DSNAAKDEEI TELKTNIEAL THAYKELRDM
     HEKLYEEHQQ MLDKQ
//