COPD_HUMAN
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 03-AUG-2022, entry version 185.
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 SRMMD.
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, rhizomelic, with microcephaly, micrognathia,
CC and developmental delay (SRMMD) [MIM:617164]: A disorder characterized
CC by facial dysmorphism, severe micrognathia, microcephaly, rhizomelic
CC short stature, and mild developmental delay.
CC {ECO:0000269|PubMed:27476655}. Note=The disease is caused by variants
CC affecting the gene represented in this entry. the skeletal phenotype,
CC that characterizes this disorder, may be due to defective type I
CC collagen transport and reduction of collagen secretion.
CC {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};
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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; 153.
DR DIP; DIP-50375N; -.
DR IntAct; P48444; 51.
DR MINT; P48444; -.
DR STRING; 9606.ENSP00000264028; -.
DR GlyGen; P48444; 5 sites, 1 O-linked glycan (5 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; P48444; -.
DR PeptideAtlas; P48444; -.
DR PRIDE; P48444; -.
DR ProteomicsDB; 19961; -.
DR ProteomicsDB; 55891; -. [P48444-1]
DR Antibodypedia; 32504; 215 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 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 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; 765 hits in 1078 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 204 other tissues.
DR ExpressionAtlas; P48444; baseline and differential.
DR Genevisible; P48444; HS.
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 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; PTHR10121; 1.
DR Pfam; PF00928; Adap_comp_sub; 1.
DR Pfam; PF01217; Clat_adaptor_s; 1.
DR SUPFAM; SSF49447; SSF49447; 1.
DR SUPFAM; SSF64356; SSF64356; 1.
DR PROSITE; PS51072; MHD; 1.
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
