ID   AP3D_YEAST              Reviewed;         932 AA.
AC   Q08951; D6W3H3; Q02737; Q7LIB1;
DT   21-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   27-MAR-2024, entry version 177.
DE   RecName: Full=AP-3 complex subunit delta;
DE   AltName: Full=Adaptor-related protein complex 3 subunit delta;
DE   AltName: Full=Delta-adaptin 3;
DE            Short=Delta-adaptin;
GN   Name=APL5; Synonyms=YKS4; OrderedLocusNames=YPL195W;
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=9169875;
RA   Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA   Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA   Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA   Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA   DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA   Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA   Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA   Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA   Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA   Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA   Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA   Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA   Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA   Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA   Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA   Vo D.H., Hani J.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL   Nature 387:103-105(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 [GENOMIC DNA] OF 8-932.
RA   Robinson L.C., Engle H.M., Panek H.R.;
RT   "Suppressors of loss of yeast casein kinase 1 function define the four
RT   subunits of a novel putative adaptin complex.";
RL   Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   IDENTIFICATION OF THE AP-3 COMPLEX, AND FUNCTION OF THE AP-3 COMPLEX.
RX   PubMed=9335339; DOI=10.1016/s0092-8674(01)80013-1;
RA   Cowles C.R., Odorizzi G., Payne G.S., Emr S.D.;
RT   "The AP-3 adaptor complex is essential for cargo-selective transport to the
RT   yeast vacuole.";
RL   Cell 91:109-118(1997).
RN   [5]
RP   IDENTIFICATION OF THE AP-3 COMPLEX, AND FUNCTION OF THE AP-3 COMPLEX.
RX   PubMed=9250663; DOI=10.1093/emboj/16.14.4194;
RA   Panek H.R., Stepp J.D., Engle H.M., Marks K.M., Tan P.K., Lemmon S.K.,
RA   Robinson L.C.;
RT   "Suppressors of YCK-encoded yeast casein kinase 1 deficiency define the
RT   four subunits of a novel clathrin AP-like complex.";
RL   EMBO J. 16:4194-4204(1997).
RN   [6]
RP   SUBCELLULAR LOCATION, INTERACTION WITH VPS41, AND FUNCTION OF THE AP-3
RP   COMPLEX.
RX   PubMed=10559961; DOI=10.1038/14037;
RA   Rehling P., Darsow T., Katzmann D.J., Emr S.D.;
RT   "Formation of AP-3 transport intermediates requires Vps41 function.";
RL   Nat. Cell Biol. 1:346-353(1999).
RN   [7]
RP   INTERACTION WITH VPS41.
RX   PubMed=11160821; DOI=10.1091/mbc.12.1.37;
RA   Darsow T., Katzmann D.J., Cowles C.R., Emr S.D.;
RT   "Vps41p function in the alkaline phosphatase pathway requires homo-
RT   oligomerization and interaction with AP-3 through two distinct domains.";
RL   Mol. Biol. Cell 12:37-51(2001).
RN   [8]
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   [9]
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   [10]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-767; SER-888 AND SER-918, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=ADR376;
RX   PubMed=17330950; DOI=10.1021/pr060559j;
RA   Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA   Elias J.E., Gygi S.P.;
RT   "Large-scale phosphorylation analysis of alpha-factor-arrested
RT   Saccharomyces cerevisiae.";
RL   J. Proteome Res. 6:1190-1197(2007).
RN   [11]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-727; SER-798 AND SER-918, AND
RP   IDENTIFICATION BY 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   [12]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-700; THR-767; SER-770;
RP   SER-773; SER-798; SER-888 AND SER-918, AND IDENTIFICATION BY MASS
RP   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).
RN   [13]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT THR-2, CLEAVAGE OF INITIATOR
RP   METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP   [LARGE SCALE ANALYSIS].
RX   PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA   Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA   Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA   Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT   "N-terminal acetylome analyses and functional insights of the N-terminal
RT   acetyltransferase NatB.";
RL   Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC   -!- FUNCTION: Part of the AP-3 complex, an adaptor-related complex which is
CC       not clathrin-associated. The complex is associated with the Golgi
CC       region as well as more peripheral structures. It facilitates the
CC       budding of vesicles from the Golgi membrane and may be directly
CC       involved in trafficking to the vacuole. Required for the transport via
CC       the ALP pathway, which directs the transport of the cargo proteins PHO8
CC       and VAM3 to the vacuole. {ECO:0000269|PubMed:10559961,
CC       ECO:0000269|PubMed:9250663, ECO:0000269|PubMed:9335339}.
CC   -!- SUBUNIT: Adaptor protein complex 3 (AP-3) is a heterotetramer composed
CC       of 2 large adaptins (APL5 and APL6), a medium adaptin (APM3) and a
CC       small adaptin (APS3). Interacts with VPS41.
CC       {ECO:0000269|PubMed:10559961, ECO:0000269|PubMed:11160821}.
CC   -!- INTERACTION:
CC       Q08951; P46682: APL6; NbExp=5; IntAct=EBI-29702, EBI-2213;
CC       Q08951; P38153: APM3; NbExp=4; IntAct=EBI-29702, EBI-2710;
CC   -!- SUBCELLULAR LOCATION: Golgi apparatus {ECO:0000269|PubMed:10559961,
CC       ECO:0000269|PubMed:14562095}. Cytoplasmic vesicle, clathrin-coated
CC       vesicle membrane {ECO:0000269|PubMed:10559961}; Peripheral membrane
CC       protein {ECO:0000305|PubMed:10559961}; Cytoplasmic side
CC       {ECO:0000305|PubMed:10559961}. Note=Component of the coat surrounding
CC       the cytoplasmic face of coated vesicles located at the Golgi complex.
CC       {ECO:0000269|PubMed:10559961}.
CC   -!- MISCELLANEOUS: Present with 13500 molecules/cell in log phase SD
CC       medium. {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the adaptor complexes large subunit family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA79850.1; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; Z73551; CAA97908.1; -; Genomic_DNA.
DR   EMBL; U36858; AAA79850.1; ALT_FRAME; Genomic_DNA.
DR   EMBL; BK006949; DAA11239.1; -; Genomic_DNA.
DR   PIR; S65214; S65214.
DR   RefSeq; NP_015129.1; NM_001184009.1.
DR   PDB; 7P3X; EM; 9.10 A; A=1-932.
DR   PDB; 7P3Y; EM; 10.10 A; A=1-932.
DR   PDB; 7P3Z; EM; 10.50 A; A=1-932.
DR   PDBsum; 7P3X; -.
DR   PDBsum; 7P3Y; -.
DR   PDBsum; 7P3Z; -.
DR   AlphaFoldDB; Q08951; -.
DR   EMDB; EMD-13187; -.
DR   EMDB; EMD-13188; -.
DR   EMDB; EMD-13189; -.
DR   SMR; Q08951; -.
DR   BioGRID; 35988; 669.
DR   ComplexPortal; CPX-535; Adapter complex AP-3.
DR   DIP; DIP-3977N; -.
DR   IntAct; Q08951; 7.
DR   MINT; Q08951; -.
DR   STRING; 4932.YPL195W; -.
DR   GlyGen; Q08951; 1 site, 1 O-linked glycan (1 site).
DR   iPTMnet; Q08951; -.
DR   MaxQB; Q08951; -.
DR   PaxDb; 4932-YPL195W; -.
DR   PeptideAtlas; Q08951; -.
DR   EnsemblFungi; YPL195W_mRNA; YPL195W; YPL195W.
DR   GeneID; 855906; -.
DR   KEGG; sce:YPL195W; -.
DR   AGR; SGD:S000006116; -.
DR   SGD; S000006116; APL5.
DR   VEuPathDB; FungiDB:YPL195W; -.
DR   eggNOG; KOG1059; Eukaryota.
DR   GeneTree; ENSGT00550000075067; -.
DR   HOGENOM; CLU_001908_1_1_1; -.
DR   InParanoid; Q08951; -.
DR   OMA; SGNNWMA; -.
DR   OrthoDB; 2877445at2759; -.
DR   BioCyc; YEAST:G3O-34088-MONOMER; -.
DR   BioGRID-ORCS; 855906; 1 hit in 10 CRISPR screens.
DR   PRO; PR:Q08951; -.
DR   Proteomes; UP000002311; Chromosome XVI.
DR   RNAct; Q08951; Protein.
DR   GO; GO:0030123; C:AP-3 adaptor complex; IMP:SGD.
DR   GO; GO:0030665; C:clathrin-coated vesicle membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0010008; C:endosome membrane; IBA:GO_Central.
DR   GO; GO:0005794; C:Golgi apparatus; IEA:UniProtKB-SubCell.
DR   GO; GO:0006896; P:Golgi to vacuole transport; IMP:SGD.
DR   GO; GO:0006886; P:intracellular protein transport; NAS:ComplexPortal.
DR   GO; GO:0006623; P:protein targeting to vacuole; IMP:SGD.
DR   Gene3D; 1.25.10.10; Leucine-rich Repeat Variant; 1.
DR   InterPro; IPR017105; AP3_complex_dsu.
DR   InterPro; IPR011989; ARM-like.
DR   InterPro; IPR016024; ARM-type_fold.
DR   InterPro; IPR002553; Clathrin/coatomer_adapt-like_N.
DR   PANTHER; PTHR22781:SF12; AP-3 COMPLEX SUBUNIT DELTA-1; 1.
DR   PANTHER; PTHR22781; DELTA ADAPTIN-RELATED; 1.
DR   Pfam; PF01602; Adaptin_N; 1.
DR   PIRSF; PIRSF037092; AP3_complex_delta; 1.
DR   SUPFAM; SSF48371; ARM repeat; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Acetylation; Coiled coil; Cytoplasmic vesicle;
KW   Golgi apparatus; Membrane; Phosphoprotein; Protein transport;
KW   Reference proteome; Repeat; Transport.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0007744|PubMed:22814378"
FT   CHAIN           2..932
FT                   /note="AP-3 complex subunit delta"
FT                   /id="PRO_0000227676"
FT   REPEAT          157..194
FT                   /note="HEAT 1"
FT   REPEAT          196..231
FT                   /note="HEAT 2"
FT   REPEAT          233..269
FT                   /note="HEAT 3"
FT   REPEAT          270..307
FT                   /note="HEAT 4"
FT   REPEAT          310..346
FT                   /note="HEAT 5"
FT   REPEAT          347..384
FT                   /note="HEAT 6"
FT   REPEAT          386..425
FT                   /note="HEAT 7"
FT   REPEAT          427..466
FT                   /note="HEAT 8"
FT   REPEAT          490..527
FT                   /note="HEAT 9"
FT   REPEAT          528..564
FT                   /note="HEAT 10"
FT   REPEAT          570..601
FT                   /note="HEAT 11"
FT   REPEAT          602..638
FT                   /note="HEAT 12"
FT   REGION          720..868
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          897..932
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          858..878
FT                   /evidence="ECO:0000255"
FT   COMPBIAS        720..764
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        765..779
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        793..836
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        838..858
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        913..932
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         2
FT                   /note="N-acetylthreonine"
FT                   /evidence="ECO:0007744|PubMed:22814378"
FT   MOD_RES         700
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         727
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   MOD_RES         767
FT                   /note="Phosphothreonine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         770
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         773
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         798
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         888
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         918
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
SQ   SEQUENCE   932 AA;  106924 MW;  51415466FF25CC40 CRC64;
     MTSLYAPGAE DIRQRLRPFG FFFEKSLKDL IKGIRSHNET PEKLDQFFKQ VLSECREEVN
     SPDLNSKTNA VLKLTYLEMY GFDMAWCNFH ILEVMSSNKL QQKRVGYLAA SQSFYKDSDI
     LMLATNLLKK DLKYDGNNDV VKVGIALSGL STIITPSLAR DIADDLFTML NSTRPYIRKK
     AITALFKVFL QYPEALRDNF DKFVSKLDDD DISVVSAAVS VICELSKKNP QPFIQLSPLL
     YEILVTIDNN WIIIRLLKLF TNLSQVEPKL RAKLLPKILE LMESTVATSV IYESVNCIVK
     GNMLEEDDFE TAMACLERLH TFCDSQDPNL RYISCILFYK IGKINTDFIS RFDQLIIRLL
     SDVDVSIRSK AIELVEGIVD EDNLKAIVQT LMKQFVDEDV VILQTGSIVY EKSKRIPIII
     PENYKIKMVN VIISICSADN YSSVNDFEWY NAVIMDLAML CQDISDKSLG SKIGEQFRNL
     MIKVPSMREV TIANIIKLIS NDNINKQLPT VLRECIWCLG EFSTLVENGN DLIKIMTENI
     SYYSHSVQEV LILALVKVFS NWCNNFQEDK RFEIKMVLKE LIEFFENLSY SSTFEVQERS
     VEVLEFLRLS LEALEEDTEG LPMLLSEVLP SFFNAYELAP IARGTQLKLA VDENLDLETP
     FLTKEAADEL LDEQKSDAIS DLMSDISMDE QVELKFVDDS DTSYEEKEKL DDFENPFEIE
     REKERMSNPY YLGEEDEERT KNSKDLLDLN EEESSDKKPE TIRLNRTDNS LNSLSLSTTE
     ISRKKKKGKK KNRVQVLSDE PVIEAAPKRK DAFQKPHDNH STQNPLKKDK INLRMHSQLE
     NFDFSNFGQS SNAGRGSQEE GNLRKEDELE LSRLEANLIV KDEKDNLSDT EEVIVIKKKK
     KGKKSKSKNK LKTKAKNSPE PNEFLRDQST DI
//