ID COPD_HUMAN Reviewed; 511 AA. AC P48444; B4E1X2; E9PEU4; Q52M80; DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot. DT 01-FEB-1996, sequence version 1. DT 27-MAR-2024, entry version 194. DE RecName: Full=Coatomer subunit delta; DE AltName: Full=Archain; DE AltName: Full=Delta-coat protein; DE Short=Delta-COP; GN Name=ARCN1; Synonyms=COPD; OS Homo sapiens (Human). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. OX NCBI_TaxID=9606; RN [1] RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1). RX PubMed=7782067; DOI=10.1016/0888-7543(95)80087-3; RA Radice P., Pensotti V., Jones C., Perry H., Pierotti M.A., Tunnacliffe A.; RT "The human archain gene, ARCN1, has highly conserved homologs in rice and RT Drosophila."; RL Genomics 26:101-106(1995). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). RC TISSUE=Trachea; RX PubMed=14702039; DOI=10.1038/ng1285; RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S., RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., RA Isogai T., Sugano S.; RT "Complete sequencing and characterization of 21,243 full-length human RT cDNAs."; RL Nat. Genet. 36:40-45(2004). RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RX PubMed=16554811; DOI=10.1038/nature04632; RA Taylor T.D., Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K., RA Lloyd C., Itoh T., Takeda T., Kim D.-W., She X., Barlow K.F., Bloom T., RA Bruford E., Chang J.L., Cuomo C.A., Eichler E., FitzGerald M.G., RA Jaffe D.B., LaButti K., Nicol R., Park H.-S., Seaman C., Sougnez C., RA Yang X., Zimmer A.R., Zody M.C., Birren B.W., Nusbaum C., Fujiyama A., RA Hattori M., Rogers J., Lander E.S., Sakaki Y.; RT "Human chromosome 11 DNA sequence and analysis including novel gene RT identification."; RL Nature 440:497-500(2006). RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). RC TISSUE=Brain; RX PubMed=15489334; DOI=10.1101/gr.2596504; RG The MGC Project Team; RT "The status, quality, and expansion of the NIH full-length cDNA project: RT the Mammalian Gene Collection (MGC)."; RL Genome Res. 14:2121-2127(2004). RN [5] RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-233 AND LYS-309, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=19608861; DOI=10.1126/science.1175371; RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., RA Olsen J.V., Mann M.; RT "Lysine acetylation targets protein complexes and co-regulates major RT cellular functions."; RL Science 325:834-840(2009). RN [6] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-493, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Cervix carcinoma; RX PubMed=20068231; DOI=10.1126/scisignal.2000475; RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.; RT "Quantitative phosphoproteomics reveals widespread full phosphorylation RT site occupancy during mitosis."; RL Sci. Signal. 3:RA3-RA3(2010). RN [7] RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=21269460; DOI=10.1186/1752-0509-5-17; RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., RA Bennett K.L., Superti-Furga G., Colinge J.; RT "Initial characterization of the human central proteome."; RL BMC Syst. Biol. 5:17-17(2011). RN [8] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-493, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=21406692; DOI=10.1126/scisignal.2001570; RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.; RT "System-wide temporal characterization of the proteome and phosphoproteome RT of human embryonic stem cell differentiation."; RL Sci. Signal. 4:RS3-RS3(2011). RN [9] RP CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION RP BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=22223895; DOI=10.1074/mcp.m111.015131; RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., RA Giglione C.; RT "Comparative large-scale characterisation of plant vs. mammal proteins RT reveals similar and idiosyncratic N-alpha acetylation features."; RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012). RN [10] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-223; SER-244 AND SER-493, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Cervix carcinoma, and Erythroleukemia; RX PubMed=23186163; DOI=10.1021/pr300630k; RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J., RA Mohammed S.; RT "Toward a comprehensive characterization of a human cancer cell RT phosphoproteome."; RL J. Proteome Res. 12:260-271(2013). RN [11] RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC TISSUE=Liver; RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014; RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., RA Ye M., Zou H.; RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver RT phosphoproteome."; RL J. Proteomics 96:253-262(2014). RN [12] RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=25944712; DOI=10.1002/pmic.201400617; RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D., RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.; RT "N-terminome analysis of the human mitochondrial proteome."; RL Proteomics 15:2519-2524(2015). RN [13] RP INVOLVEMENT IN SSMG. RX PubMed=27476655; DOI=10.1016/j.ajhg.2016.06.011; RA Izumi K., Brett M., Nishi E., Drunat S., Tan E.S., Fujiki K., Lebon S., RA Cham B., Masuda K., Arakawa M., Jacquinet A., Yamazumi Y., Chen S.T., RA Verloes A., Okada Y., Katou Y., Nakamura T., Akiyama T., Gressens P., RA Foo R., Passemard S., Tan E.C., El Ghouzzi V., Shirahige K.; RT "ARCN1 mutations cause a recognizable craniofacial syndrome due to copi- RT mediated transport defects."; RL Am. J. Hum. Genet. 99:451-459(2016). CC -!- FUNCTION: Component of the coatomer, a cytosolic protein complex that CC binds to dilysine motifs and reversibly associates with Golgi non- CC clathrin-coated vesicles, which further mediate biosynthetic protein CC transport from the ER, via the Golgi up to the trans Golgi network. The CC coatomer complex is required for budding from Golgi membranes, and is CC essential for the retrograde Golgi-to-ER transport of dilysine-tagged CC proteins. In mammals, the coatomer can only be recruited by membranes CC associated to ADP-ribosylation factors (ARFs), which are small GTP- CC binding proteins; the complex also influences the Golgi structural CC integrity, as well as the processing, activity, and endocytic recycling CC of LDL receptors (By similarity). {ECO:0000250}. CC -!- SUBUNIT: Oligomeric complex that consists of at least the alpha, beta, CC beta', gamma, delta, epsilon and zeta subunits. CC -!- INTERACTION: CC P48444; P53618: COPB1; NbExp=3; IntAct=EBI-1044491, EBI-359063; CC P48444; P42858: HTT; NbExp=3; IntAct=EBI-1044491, EBI-466029; CC P48444; Q9BQE6-2: LBHD1; NbExp=3; IntAct=EBI-1044491, EBI-12277798; CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Golgi apparatus membrane CC {ECO:0000250}; Peripheral membrane protein {ECO:0000250}; Cytoplasmic CC side {ECO:0000250}. Cytoplasmic vesicle, COPI-coated vesicle membrane CC {ECO:0000250}; Peripheral membrane protein {ECO:0000250}; Cytoplasmic CC side {ECO:0000250}. Note=The coatomer is cytoplasmic or polymerized on CC the cytoplasmic side of the Golgi, as well as on the vesicles/buds CC originating from it. {ECO:0000250}. CC -!- ALTERNATIVE PRODUCTS: CC Event=Alternative splicing; Named isoforms=2; CC Name=1; CC IsoId=P48444-1; Sequence=Displayed; CC Name=2; CC IsoId=P48444-2; Sequence=VSP_045636; CC -!- TISSUE SPECIFICITY: Ubiquitously expressed. CC -!- DISEASE: Short stature-micrognathia syndrome (SSMG) [MIM:617164]: An CC autosomal dominant disorder characterized by facial dysmorphism, severe CC micrognathia, microcephaly, rhizomelic short stature, and mild CC developmental delay. {ECO:0000269|PubMed:27476655}. Note=The disease is CC caused by variants affecting the gene represented in this entry. the CC skeletal phenotype, that characterizes this disorder, may be due to CC defective type I collagen transport and reduction of collagen CC secretion. {ECO:0000269|PubMed:27476655}. CC -!- SIMILARITY: Belongs to the adaptor complexes medium subunit family. CC Delta-COP subfamily. {ECO:0000305}. CC -!- SEQUENCE CAUTION: CC Sequence=CAA57072.1; Type=Erroneous initiation; Evidence={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; X81197; CAA57071.1; -; mRNA. DR EMBL; X81198; CAA57072.1; ALT_INIT; mRNA. DR EMBL; AK304019; BAG64934.1; -; mRNA. DR EMBL; AP000941; -; NOT_ANNOTATED_CDS; Genomic_DNA. DR EMBL; BC093636; AAH93636.1; -; mRNA. DR EMBL; BC093638; AAH93638.1; -; mRNA. DR CCDS; CCDS44749.1; -. [P48444-2] DR CCDS; CCDS8400.1; -. [P48444-1] DR PIR; A56750; A56750. DR RefSeq; NP_001135753.1; NM_001142281.1. [P48444-2] DR RefSeq; NP_001646.2; NM_001655.4. [P48444-1] DR AlphaFoldDB; P48444; -. DR SMR; P48444; -. DR BioGRID; 106867; 222. DR ComplexPortal; CPX-7803; COPI vesicle coat complex, COPG1-COPZ1 variant. DR ComplexPortal; CPX-7969; COPI vesicle coat complex, COPG2-COPZ1 variant. DR ComplexPortal; CPX-7970; COPI vesicle coat complex, COPG1-COPZ2 variant. DR DIP; DIP-50375N; -. DR IntAct; P48444; 69. DR MINT; P48444; -. DR STRING; 9606.ENSP00000264028; -. DR GlyCosmos; P48444; 5 sites, 1 glycan. DR GlyGen; P48444; 6 sites, 1 O-linked glycan (6 sites). DR iPTMnet; P48444; -. DR MetOSite; P48444; -. DR PhosphoSitePlus; P48444; -. DR SwissPalm; P48444; -. DR BioMuta; ARCN1; -. DR DMDM; 1351970; -. DR OGP; P48444; -. DR EPD; P48444; -. DR jPOST; P48444; -. DR MassIVE; P48444; -. DR MaxQB; P48444; -. DR PaxDb; 9606-ENSP00000264028; -. DR PeptideAtlas; P48444; -. DR ProteomicsDB; 19961; -. DR ProteomicsDB; 55891; -. [P48444-1] DR Pumba; P48444; -. DR Antibodypedia; 32504; 235 antibodies from 24 providers. DR DNASU; 372; -. DR Ensembl; ENST00000264028.5; ENSP00000264028.4; ENSG00000095139.15. [P48444-1] DR Ensembl; ENST00000392859.7; ENSP00000376599.3; ENSG00000095139.15. [P48444-2] DR GeneID; 372; -. DR KEGG; hsa:372; -. DR MANE-Select; ENST00000264028.5; ENSP00000264028.4; NM_001655.5; NP_001646.2. DR UCSC; uc001ptq.4; human. [P48444-1] DR AGR; HGNC:649; -. DR CTD; 372; -. DR DisGeNET; 372; -. DR GeneCards; ARCN1; -. DR HGNC; HGNC:649; ARCN1. DR HPA; ENSG00000095139; Low tissue specificity. DR MalaCards; ARCN1; -. DR MIM; 600820; gene. DR MIM; 617164; phenotype. DR neXtProt; NX_P48444; -. DR OpenTargets; ENSG00000095139; -. DR PharmGKB; PA24931; -. DR VEuPathDB; HostDB:ENSG00000095139; -. DR eggNOG; KOG2635; Eukaryota. DR GeneTree; ENSGT00390000017207; -. DR HOGENOM; CLU_019988_2_0_1; -. DR InParanoid; P48444; -. DR OMA; YDARKHV; -. DR OrthoDB; 205756at2759; -. DR PhylomeDB; P48444; -. DR TreeFam; TF105760; -. DR PathwayCommons; P48444; -. DR Reactome; R-HSA-6807878; COPI-mediated anterograde transport. DR Reactome; R-HSA-6811434; COPI-dependent Golgi-to-ER retrograde traffic. DR SignaLink; P48444; -. DR BioGRID-ORCS; 372; 799 hits in 1156 CRISPR screens. DR ChiTaRS; ARCN1; human. DR GenomeRNAi; 372; -. DR Pharos; P48444; Tbio. DR PRO; PR:P48444; -. DR Proteomes; UP000005640; Chromosome 11. DR RNAct; P48444; Protein. DR Bgee; ENSG00000095139; Expressed in islet of Langerhans and 206 other cell types or tissues. DR ExpressionAtlas; P48444; baseline and differential. DR GO; GO:0030126; C:COPI vesicle coat; ISS:UniProtKB. DR GO; GO:0005829; C:cytosol; TAS:Reactome. DR GO; GO:0005789; C:endoplasmic reticulum membrane; TAS:Reactome. DR GO; GO:0000139; C:Golgi membrane; TAS:Reactome. DR GO; GO:0016020; C:membrane; HDA:UniProtKB. DR GO; GO:0030133; C:transport vesicle; TAS:Reactome. DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB. DR GO; GO:0008344; P:adult locomotory behavior; IEA:Ensembl. DR GO; GO:0021691; P:cerebellar Purkinje cell layer maturation; IEA:Ensembl. DR GO; GO:0006888; P:endoplasmic reticulum to Golgi vesicle-mediated transport; IBA:GO_Central. DR GO; GO:0051645; P:Golgi localization; IBA:GO_Central. DR GO; GO:0006886; P:intracellular protein transport; TAS:ProtInc. DR GO; GO:0043473; P:pigmentation; IEA:Ensembl. DR GO; GO:0006890; P:retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum; IBA:GO_Central. DR CDD; cd09254; AP_delta-COPI_MHD; 1. DR CDD; cd14830; Delta_COP_N; 1. DR Gene3D; 3.30.450.60; -; 1. DR Gene3D; 2.60.40.1170; Mu homology domain, subdomain B; 2. DR InterPro; IPR036168; AP2_Mu_C_sf. DR InterPro; IPR022775; AP_mu_sigma_su. DR InterPro; IPR027059; Coatomer_dsu. DR InterPro; IPR011012; Longin-like_dom_sf. DR InterPro; IPR028565; MHD. DR PANTHER; PTHR10121; COATOMER SUBUNIT DELTA; 1. DR PANTHER; PTHR10121:SF0; COATOMER SUBUNIT DELTA; 1. DR Pfam; PF00928; Adap_comp_sub; 1. DR Pfam; PF01217; Clat_adaptor_s; 1. DR SUPFAM; SSF49447; Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor; 1. DR SUPFAM; SSF64356; SNARE-like; 1. DR PROSITE; PS51072; MHD; 1. DR Genevisible; P48444; HS. PE 1: Evidence at protein level; KW Acetylation; Alternative splicing; Cytoplasm; Cytoplasmic vesicle; KW Dwarfism; ER-Golgi transport; Golgi apparatus; Membrane; Phosphoprotein; KW Protein transport; Reference proteome; Transport. FT INIT_MET 1 FT /note="Removed" FT /evidence="ECO:0007744|PubMed:22223895" FT CHAIN 2..511 FT /note="Coatomer subunit delta" FT /id="PRO_0000193841" FT DOMAIN 271..511 FT /note="MHD" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00404" FT REGION 168..188 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOD_RES 223 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:23186163" FT MOD_RES 233 FT /note="N6-acetyllysine" FT /evidence="ECO:0007744|PubMed:19608861" FT MOD_RES 241 FT /note="N6-acetyllysine" FT /evidence="ECO:0000250|UniProtKB:Q5XJY5" FT MOD_RES 244 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:23186163" FT MOD_RES 309 FT /note="N6-acetyllysine" FT /evidence="ECO:0007744|PubMed:19608861" FT MOD_RES 351 FT /note="N6-acetyllysine" FT /evidence="ECO:0000250|UniProtKB:Q5XJY5" FT MOD_RES 493 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:20068231, FT ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163" FT VAR_SEQ 1..89 FT /note="MVLLAAAVCTKAGKAIVSRQFVEMTRTRIEGLLAAFPKLMNTGKQHTFVETE FT SVRYVYQPMEKLYMVLITTKNSNILEDLETLRLFSRV -> M (in isoform 2)" FT /evidence="ECO:0000303|PubMed:14702039" FT /id="VSP_045636" FT VARIANT 186 FT /note="F -> L (in dbSNP:rs682327)" FT /id="VAR_011788" FT VARIANT 309 FT /note="K -> N (in dbSNP:rs1063124)" FT /id="VAR_011789" FT CONFLICT 387 FT /note="N -> D (in Ref. 2; BAG64934)" FT /evidence="ECO:0000305" SQ SEQUENCE 511 AA; 57210 MW; 4ED1F7D2D12A7F75 CRC64; MVLLAAAVCT KAGKAIVSRQ FVEMTRTRIE GLLAAFPKLM NTGKQHTFVE TESVRYVYQP MEKLYMVLIT TKNSNILEDL ETLRLFSRVI PEYCRALEEN EISEHCFDLI FAFDEIVALG YRENVNLAQI RTFTEMDSHE EKVFRAVRET QEREAKAEMR RKAKELQQAR RDAERQGKKA PGFGGFGSSA VSGGSTAAMI TETIIETDKP KVAPAPARPS GPSKALKLGA KGKEVDNFVD KLKSEGETIM SSSMGKRTSE ATKMHAPPIN MESVHMKIEE KITLTCGRDG GLQNMELHGM IMLRISDDKY GRIRLHVENE DKKGVQLQTH PNVDKKLFTA ESLIGLKNPE KSFPVNSDVG VLKWRLQTTE ESFIPLTINC WPSESGNGCD VNIEYELQED NLELNDVVIT IPLPSGVGAP VIGEIDGEYR HDSRRNTLEW CLPVIDAKNK SGSLEFSIAG QPNDFFPVQV SFVSKKNYCN IQVTKVTQVD GNSPVRFSTE TTFLVDKYEI L //