CCD47_MOUSE
ID CCD47_MOUSE Reviewed; 483 AA.
AC Q9D024; B1AR94; Q3TSB5; Q3V1S7; Q8C5D9; Q920S6;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=PAT complex subunit CCDC47 {ECO:0000250|UniProtKB:Q96A33};
DE AltName: Full=Adipocyte-specific protein 4 {ECO:0000303|Ref.1};
DE AltName: Full=Calumin {ECO:0000303|PubMed:25009997};
DE AltName: Full=Coiled-coil domain-containing protein 47;
DE Flags: Precursor;
GN Name=Ccdc47 {ECO:0000312|MGI:MGI:1914413};
GN Synonyms=Asp4 {ECO:0000303|Ref.1};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RA Tsuruga H.;
RT "Adipocyte-specific protein 4, a novel protein upregulated during adipocyte
RT differentiation.";
RL Submitted (MAR-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3).
RC STRAIN=C57BL/6J; TISSUE=Egg, Embryo, Lung, and Placenta;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas,
RC Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH VCP;
RP HSPA5; DERL1; DERL2 AND SELENOS, AND DISRUPTION PHENOTYPE.
RX PubMed=25009997; DOI=10.1016/j.ydbio.2014.06.024;
RA Yamamoto S., Yamazaki T., Komazaki S., Yamashita T., Osaki M.,
RA Matsubayashi M., Kidoya H., Takakura N., Yamazaki D., Kakizawa S.;
RT "Contribution of calumin to embryogenesis through participation in the
RT endoplasmic reticulum-associated degradation activity.";
RL Dev. Biol. 393:33-43(2014).
CC -!- FUNCTION: Component of the PAT complex, an endoplasmic reticulum (ER)-
CC resident membrane multiprotein complex that facilitates multi-pass
CC membrane proteins insertion into membranes. The PAT complex acts as an
CC intramembrane chaperone by directly interacting with nascent
CC transmembrane domains (TMDs), releasing its substrates upon correct
CC folding, and is needed for optimal biogenesis of multi-pass membrane
CC proteins. WDR83OS/Asterix is the substrate-interacting subunit of the
CC PAT complex, whereas CCDC47 is required to maintain the stability of
CC WDR83OS/Asterix. The PAT complex favors the binding to TMDs with
CC exposed hydrophilic amino acids within the lipid bilayer and provides a
CC membrane-embedded partially hydrophilic environment in which the first
CC transmembrane domain binds. Component of a ribosome-associated ER
CC translocon complex involved in multi-pass membrane protein transport
CC into the ER membrane and biogenesis. Involved in the regulation of
CC calcium ion homeostasis in the ER. Required for proper protein
CC degradation via the ERAD (ER-associated degradation) pathway (By
CC similarity). Has an essential role in the maintenance of ER
CC organization during embryogenesis (PubMed:25009997).
CC {ECO:0000250|UniProtKB:Q96A33, ECO:0000269|PubMed:25009997}.
CC -!- SUBUNIT: The PAT complex includes WDR83OS/Asterix and CCDC47. The
CC ribosome-associated ER translocon complex includes SEC61A1, SEC61B,
CC SEC61G, TMCO1, CCDC47, NCLN/Nicalin, NOMO and TMEM147; in the absence
CC of ribosomes, only the complex forms with NCLN/Nicalin, NOMO and
CC TMEM147 remains intact (By similarity). Interacts with VCP, HSPA5,
CC DERL1, DERL2 and SELENOS (PubMed:25009997).
CC {ECO:0000250|UniProtKB:Q96A33, ECO:0000269|PubMed:25009997}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000250|UniProtKB:Q96A33}; Single-pass membrane protein
CC {ECO:0000305}. Rough endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:25009997}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9D024-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9D024-2; Sequence=VSP_018480;
CC Name=3;
CC IsoId=Q9D024-3; Sequence=VSP_018479;
CC -!- TISSUE SPECIFICITY: In the embryo, expressed in the endodermal layer of
CC the yolk sac and in the small intestine. {ECO:0000269|PubMed:25009997}.
CC -!- DISRUPTION PHENOTYPE: CCDC47 knockout leads to embryonic lethality at
CC mid-gestation, between 10.5 and 11.5 dpc. Mutant embryos at 8.5-10.5
CC dpc reveal several anomalies including vascular abnormalities in yolk
CC sacs, developmental retardation, atrophic neural tubes, dilated left
CC ventricles, poorly developed myocardium, and paucity of blood cells in
CC the dorsal aorta. Yolk sac endoderm cells show alterations associated
CC with endoplasmic reticulum stress, including lipid droplet
CC accumulation, endoplasmic reticulum fragmentation and dissociation of
CC ribosomes. {ECO:0000269|PubMed:25009997}.
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DR EMBL; AB040489; BAB68502.1; -; mRNA.
DR EMBL; AK011882; BAB27896.1; -; mRNA.
DR EMBL; AK078812; BAC37406.1; -; mRNA.
DR EMBL; AK132273; BAE21073.1; -; mRNA.
DR EMBL; AK162160; BAE36760.1; -; mRNA.
DR EMBL; AL596331; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR CCDS; CCDS25551.1; -. [Q9D024-1]
DR RefSeq; NP_080285.2; NM_026009.2. [Q9D024-1]
DR AlphaFoldDB; Q9D024; -.
DR SMR; Q9D024; -.
DR BioGRID; 211988; 4.
DR STRING; 10090.ENSMUSP00000002043; -.
DR GlyGen; Q9D024; 1 site.
DR iPTMnet; Q9D024; -.
DR PhosphoSitePlus; Q9D024; -.
DR SwissPalm; Q9D024; -.
DR EPD; Q9D024; -.
DR jPOST; Q9D024; -.
DR MaxQB; Q9D024; -.
DR PaxDb; Q9D024; -.
DR PeptideAtlas; Q9D024; -.
DR PRIDE; Q9D024; -.
DR ProteomicsDB; 281500; -. [Q9D024-1]
DR ProteomicsDB; 281501; -. [Q9D024-2]
DR ProteomicsDB; 281502; -. [Q9D024-3]
DR Antibodypedia; 31338; 176 antibodies from 24 providers.
DR Ensembl; ENSMUST00000002043; ENSMUSP00000002043; ENSMUSG00000078622. [Q9D024-1]
DR Ensembl; ENSMUST00000106865; ENSMUSP00000102478; ENSMUSG00000078622. [Q9D024-3]
DR GeneID; 67163; -.
DR KEGG; mmu:67163; -.
DR UCSC; uc007lyi.1; mouse. [Q9D024-1]
DR UCSC; uc007lyj.1; mouse. [Q9D024-2]
DR CTD; 57003; -.
DR MGI; MGI:1914413; Ccdc47.
DR VEuPathDB; HostDB:ENSMUSG00000078622; -.
DR eggNOG; KOG2357; Eukaryota.
DR GeneTree; ENSGT00390000013997; -.
DR HOGENOM; CLU_033196_1_0_1; -.
DR InParanoid; Q9D024; -.
DR OMA; PPIDQKV; -.
DR PhylomeDB; Q9D024; -.
DR TreeFam; TF314902; -.
DR BioGRID-ORCS; 67163; 5 hits in 73 CRISPR screens.
DR ChiTaRS; Ccdc47; mouse.
DR PRO; PR:Q9D024; -.
DR Proteomes; UP000000589; Chromosome 11.
DR RNAct; Q9D024; protein.
DR Bgee; ENSMUSG00000078622; Expressed in ciliary body and 238 other tissues.
DR ExpressionAtlas; Q9D024; baseline and differential.
DR Genevisible; Q9D024; MM.
DR GO; GO:0101031; C:chaperone complex; ISO:MGI.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:MGI.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; ISO:MGI.
DR GO; GO:0030176; C:integral component of endoplasmic reticulum membrane; ISS:UniProtKB.
DR GO; GO:0005791; C:rough endoplasmic reticulum; IDA:MGI.
DR GO; GO:0030867; C:rough endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005509; F:calcium ion binding; IDA:MGI.
DR GO; GO:0044183; F:protein folding chaperone; ISS:UniProtKB.
DR GO; GO:0043022; F:ribosome binding; ISS:UniProtKB.
DR GO; GO:0055074; P:calcium ion homeostasis; IMP:MGI.
DR GO; GO:0032469; P:endoplasmic reticulum calcium ion homeostasis; ISS:UniProtKB.
DR GO; GO:0007029; P:endoplasmic reticulum organization; IMP:MGI.
DR GO; GO:0006983; P:ER overload response; IMP:MGI.
DR GO; GO:0036503; P:ERAD pathway; ISO:MGI.
DR GO; GO:0009791; P:post-embryonic development; IMP:MGI.
DR GO; GO:0045048; P:protein insertion into ER membrane; ISS:UniProtKB.
DR GO; GO:0030433; P:ubiquitin-dependent ERAD pathway; IMP:MGI.
DR InterPro; IPR012879; CCDC47.
DR PANTHER; PTHR12883; PTHR12883; 1.
DR Pfam; PF07946; DUF1682; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chaperone; Coiled coil; Endoplasmic reticulum;
KW Glycoprotein; Membrane; Reference proteome; Signal; Transmembrane;
KW Transmembrane helix.
FT SIGNAL 1..20
FT /evidence="ECO:0000255"
FT CHAIN 21..483
FT /note="PAT complex subunit CCDC47"
FT /id="PRO_0000235799"
FT TRANSMEM 136..156
FT /note="Helical"
FT /evidence="ECO:0000255"
FT REGION 46..119
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 424..483
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 450..483
FT /evidence="ECO:0000255"
FT COMPBIAS 63..106
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 424..471
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CARBOHYD 178
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT VAR_SEQ 1..316
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_018479"
FT VAR_SEQ 458..483
FT /note="EAALRREQKKLEKKQMKMKQIKVKAM -> VRHSEARLLGSASLLCGFMF
FT (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_018480"
FT CONFLICT 111
FT /note="T -> A (in Ref. 2; BAB27896/BAE36760)"
FT /evidence="ECO:0000305"
FT CONFLICT 145
FT /note="G -> S (in Ref. 2; BAC37406)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 483 AA; 55844 MW; DDD4DDFE644D65E9 CRC64;
MKAFYAFCVV LLVFGSVSEA KFDDFEDEED IVEYDDNDFA EFEDVMEDSV TESPQRVIST
EDDEDEATVE LEGQDESQEG DFEDADTQEG DTESEPYDDE EFEGYEDKPD TSSNKNKDPI
TIVDVPAHLQ NSWESYYLEI LMVTGLLAYI MNYIIGKNKN SRLAQAWFNS HRELLESNFT
LVGDDGTNKE ATSTGKLNQE NEHIYNLWCS GRVCCEGMLI QLRFLKRQDL LNVLARMMRP
VSDQVQIKVT MNDEDMDTYV FAVGTRKALL RLQKEMQDLS EFCSDKPKSG AKYGLPDSLA
ILSEMGEVTE GMMDTKMVHF LTHYADKIES VHFSDQFSGP KIMQEEGQPL KLPDTKRTLL
FTFNVPGSGN TYPKDMESLL PLMNMVIYSI DKAKKFRLNR EGKQKADKNR ARVEENFLKL
THVQRQEAAQ SRREEKKRAE KERIMNEEDP EKQRRLEEAA LRREQKKLEK KQMKMKQIKV
KAM
