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Coatomer subunit delta (Archain) (Delta-coat protein) (Delta-COP)

 COPD_HUMAN              Reviewed;         511 AA.
P48444; B4E1X2; E9PEU4; Q52M80;
01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
01-FEB-1996, sequence version 1.
20-JUN-2018, entry version 160.
RecName: Full=Coatomer subunit delta;
AltName: Full=Archain;
AltName: Full=Delta-coat protein;
Short=Delta-COP;
Name=ARCN1; Synonyms=COPD;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
PubMed=7782067; DOI=10.1016/0888-7543(95)80087-3;
Radice P., Pensotti V., Jones C., Perry H., Pierotti M.A.,
Tunnacliffe A.;
"The human archain gene, ARCN1, has highly conserved homologs in rice
and Drosophila.";
Genomics 26:101-106(1995).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
TISSUE=Trachea;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16554811; DOI=10.1038/nature04632;
Taylor T.D., Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K.,
Lloyd C., Itoh T., Takeda T., Kim D.-W., She X., Barlow K.F.,
Bloom T., Bruford E., Chang J.L., Cuomo C.A., Eichler E.,
FitzGerald M.G., Jaffe D.B., LaButti K., Nicol R., Park H.-S.,
Seaman C., Sougnez C., Yang X., Zimmer A.R., Zody M.C., Birren B.W.,
Nusbaum C., Fujiyama A., Hattori M., Rogers J., Lander E.S.,
Sakaki Y.;
"Human chromosome 11 DNA sequence and analysis including novel gene
identification.";
Nature 440:497-500(2006).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Brain;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-233 AND LYS-309, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19608861; DOI=10.1126/science.1175371;
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M.,
Walther T.C., Olsen J.V., Mann M.;
"Lysine acetylation targets protein complexes and co-regulates major
cellular functions.";
Science 325:834-840(2009).
[6]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-493, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=20068231; DOI=10.1126/scisignal.2000475;
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
Mann M.;
"Quantitative phosphoproteomics reveals widespread full
phosphorylation site occupancy during mitosis.";
Sci. Signal. 3:RA3-RA3(2010).
[7]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-493, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21406692; DOI=10.1126/scisignal.2001570;
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
Blagoev B.;
"System-wide temporal characterization of the proteome and
phosphoproteome of human embryonic stem cell differentiation.";
Sci. Signal. 4:RS3-RS3(2011).
[9]
CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22223895; DOI=10.1074/mcp.M111.015131;
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C.,
Meinnel T., Giglione C.;
"Comparative large-scale characterisation of plant vs. mammal proteins
reveals similar and idiosyncratic N-alpha acetylation features.";
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-223; SER-244 AND
SER-493, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
TISSUE=Cervix carcinoma, and Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[11]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
[12]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25944712; DOI=10.1002/pmic.201400617;
Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M.,
Ayoub D., Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
"N-terminome analysis of the human mitochondrial proteome.";
Proteomics 15:2519-2524(2015).
[13]
INVOLVEMENT IN SRMMD.
PubMed=27476655; DOI=10.1016/j.ajhg.2016.06.011;
Izumi K., Brett M., Nishi E., Drunat S., Tan E.S., Fujiki K.,
Lebon S., Cham B., Masuda K., Arakawa M., Jacquinet A., Yamazumi Y.,
Chen S.T., Verloes A., Okada Y., Katou Y., Nakamura T., Akiyama T.,
Gressens P., Foo R., Passemard S., Tan E.C., El Ghouzzi V.,
Shirahige K.;
"ARCN1 mutations cause a recognizable craniofacial syndrome due to
copi-mediated transport defects.";
Am. J. Hum. Genet. 99:451-459(2016).
-!- FUNCTION: Component of the coatomer, a cytosolic protein complex
that binds to dilysine motifs and reversibly associates with Golgi
non-clathrin-coated vesicles, which further mediate biosynthetic
protein transport from the ER, via the Golgi up to the trans Golgi
network. The coatomer complex is required for budding from Golgi
membranes, and is essential for the retrograde Golgi-to-ER
transport of dilysine-tagged proteins. In mammals, the coatomer
can only be recruited by membranes associated to ADP-ribosylation
factors (ARFs), which are small GTP-binding proteins; the complex
also influences the Golgi structural integrity, as well as the
processing, activity, and endocytic recycling of LDL receptors (By
similarity). {ECO:0000250}.
-!- SUBUNIT: Oligomeric complex that consists of at least the alpha,
beta, beta', gamma, delta, epsilon and zeta subunits.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Golgi apparatus
membrane {ECO:0000250}; Peripheral membrane protein {ECO:0000250};
Cytoplasmic side {ECO:0000250}. Cytoplasmic vesicle, COPI-coated
vesicle membrane {ECO:0000250}; Peripheral membrane protein
{ECO:0000250}; Cytoplasmic side {ECO:0000250}. Note=The coatomer
is cytoplasmic or polymerized on the cytoplasmic side of the
Golgi, as well as on the vesicles/buds originating from it.
{ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=P48444-1; Sequence=Displayed;
Name=2;
IsoId=P48444-2; Sequence=VSP_045636;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Ubiquitously expressed.
-!- DISEASE: Short stature, rhizomelic, with microcephaly,
micrognathia, and developmental delay (SRMMD) [MIM:617164]: A
disorder characterized by facial dysmorphism, severe micrognathia,
microcephaly, rhizomelic short stature, and mild developmental
delay. {ECO:0000269|PubMed:27476655}. Note=The disease is caused
by mutations affecting the gene represented in this entry. the
skeletal phenotype, that characterizes this disorder, may be due
to defective type I collagen transport and reduction of collagen
secretion. {ECO:0000269|PubMed:27476655}.
-!- SIMILARITY: Belongs to the adaptor complexes medium subunit
family. Delta-COP subfamily. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAA57072.1; Type=Erroneous initiation; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; X81197; CAA57071.1; -; mRNA.
EMBL; X81198; CAA57072.1; ALT_INIT; mRNA.
EMBL; AK304019; BAG64934.1; -; mRNA.
EMBL; AP000941; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BC093636; AAH93636.1; -; mRNA.
EMBL; BC093638; AAH93638.1; -; mRNA.
CCDS; CCDS44749.1; -. [P48444-2]
CCDS; CCDS8400.1; -. [P48444-1]
PIR; A56750; A56750.
RefSeq; NP_001135753.1; NM_001142281.1. [P48444-2]
RefSeq; NP_001646.2; NM_001655.4. [P48444-1]
UniGene; Hs.33642; -.
ProteinModelPortal; P48444; -.
BioGrid; 106867; 43.
DIP; DIP-50375N; -.
IntAct; P48444; 30.
MINT; P48444; -.
STRING; 9606.ENSP00000264028; -.
iPTMnet; P48444; -.
PhosphoSitePlus; P48444; -.
SwissPalm; P48444; -.
BioMuta; ARCN1; -.
DMDM; 1351970; -.
OGP; P48444; -.
EPD; P48444; -.
MaxQB; P48444; -.
PaxDb; P48444; -.
PeptideAtlas; P48444; -.
PRIDE; P48444; -.
ProteomicsDB; 55891; -.
Ensembl; ENST00000264028; ENSP00000264028; ENSG00000095139. [P48444-1]
Ensembl; ENST00000392859; ENSP00000376599; ENSG00000095139. [P48444-2]
GeneID; 372; -.
KEGG; hsa:372; -.
UCSC; uc001ptq.4; human. [P48444-1]
CTD; 372; -.
DisGeNET; 372; -.
EuPathDB; HostDB:ENSG00000095139.13; -.
GeneCards; ARCN1; -.
HGNC; HGNC:649; ARCN1.
HPA; HPA037573; -.
HPA; HPA044874; -.
MalaCards; ARCN1; -.
MIM; 600820; gene.
MIM; 617164; phenotype.
neXtProt; NX_P48444; -.
OpenTargets; ENSG00000095139; -.
PharmGKB; PA24931; -.
eggNOG; KOG2635; Eukaryota.
eggNOG; ENOG410XRH2; LUCA.
GeneTree; ENSGT00390000017207; -.
HOGENOM; HOG000203984; -.
HOVERGEN; HBG005381; -.
InParanoid; P48444; -.
KO; K20471; -.
PhylomeDB; P48444; -.
TreeFam; TF105760; -.
Reactome; R-HSA-6807878; COPI-mediated anterograde transport.
Reactome; R-HSA-6811434; COPI-dependent Golgi-to-ER retrograde traffic.
SignaLink; P48444; -.
ChiTaRS; ARCN1; human.
GenomeRNAi; 372; -.
PRO; PR:P48444; -.
Proteomes; UP000005640; Chromosome 11.
Bgee; ENSG00000095139; -.
CleanEx; HS_ARCN1; -.
ExpressionAtlas; P48444; baseline and differential.
Genevisible; P48444; HS.
GO; GO:0030126; C:COPI vesicle coat; ISS:UniProtKB.
GO; GO:0005829; C:cytosol; TAS:Reactome.
GO; GO:0005789; C:endoplasmic reticulum membrane; TAS:Reactome.
GO; GO:0000139; C:Golgi membrane; TAS:Reactome.
GO; GO:0016020; C:membrane; HDA:UniProtKB.
GO; GO:0030133; C:transport vesicle; TAS:Reactome.
GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
GO; GO:0008344; P:adult locomotory behavior; IEA:Ensembl.
GO; GO:0021691; P:cerebellar Purkinje cell layer maturation; IEA:Ensembl.
GO; GO:0006888; P:ER to Golgi vesicle-mediated transport; TAS:Reactome.
GO; GO:0006886; P:intracellular protein transport; TAS:ProtInc.
GO; GO:0043473; P:pigmentation; IEA:Ensembl.
GO; GO:0006890; P:retrograde vesicle-mediated transport, Golgi to ER; TAS:Reactome.
InterPro; IPR036168; AP2_Mu_C_sf.
InterPro; IPR022775; AP_mu_sigma_su.
InterPro; IPR027059; Coatomer_dsu.
InterPro; IPR011012; Longin-like_dom_sf.
InterPro; IPR028565; MHD.
PANTHER; PTHR10121; PTHR10121; 1.
Pfam; PF00928; Adap_comp_sub; 1.
Pfam; PF01217; Clat_adaptor_s; 1.
SUPFAM; SSF49447; SSF49447; 1.
SUPFAM; SSF64356; SSF64356; 1.
PROSITE; PS51072; MHD; 1.
1: Evidence at protein level;
Acetylation; Alternative splicing; Complete proteome; Cytoplasm;
Cytoplasmic vesicle; Dwarfism; ER-Golgi transport; Golgi apparatus;
Membrane; Phosphoprotein; Polymorphism; Protein transport;
Reference proteome; Transport.
INIT_MET 1 1 Removed. {ECO:0000244|PubMed:22223895}.
CHAIN 2 511 Coatomer subunit delta.
/FTId=PRO_0000193841.
DOMAIN 271 511 MHD. {ECO:0000255|PROSITE-
ProRule:PRU00404}.
MOD_RES 223 223 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
MOD_RES 233 233 N6-acetyllysine.
{ECO:0000244|PubMed:19608861}.
MOD_RES 241 241 N6-acetyllysine.
{ECO:0000250|UniProtKB:Q5XJY5}.
MOD_RES 244 244 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
MOD_RES 309 309 N6-acetyllysine.
{ECO:0000244|PubMed:19608861}.
MOD_RES 351 351 N6-acetyllysine.
{ECO:0000250|UniProtKB:Q5XJY5}.
MOD_RES 493 493 Phosphoserine.
{ECO:0000244|PubMed:20068231,
ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:23186163}.
VAR_SEQ 1 89 MVLLAAAVCTKAGKAIVSRQFVEMTRTRIEGLLAAFPKLMN
TGKQHTFVETESVRYVYQPMEKLYMVLITTKNSNILEDLET
LRLFSRV -> M (in isoform 2).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_045636.
VARIANT 186 186 F -> L (in dbSNP:rs682327).
/FTId=VAR_011788.
VARIANT 309 309 K -> N (in dbSNP:rs1063124).
/FTId=VAR_011789.
CONFLICT 387 387 N -> D (in Ref. 2; BAG64934).
{ECO:0000305}.
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


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