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T-cell surface glycoprotein CD1c (CD antigen CD1c)

 CD1C_HUMAN              Reviewed;         333 AA.
P29017; Q5TDJ7; Q6IAS4; Q9UMM0; Q9UN96;
01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
03-APR-2007, sequence version 2.
25-OCT-2017, entry version 161.
RecName: Full=T-cell surface glycoprotein CD1c;
AltName: CD_antigen=CD1c;
Flags: Precursor;
Name=CD1C;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=2447586; DOI=10.1073/pnas.84.24.9189;
Martin L.H., Calabi F., Lefebvre F.-A., Bilsland C.A.G., Milstein C.;
"Structure and expression of the human thymocyte antigens CD1a, CD1b,
and CD1c.";
Proc. Natl. Acad. Sci. U.S.A. 84:9189-9193(1987).
[2]
NUCLEOTIDE SEQUENCE [MRNA], AND VARIANT SER-300.
PubMed=2701945;
Aruffo A., Seed B.;
"Expression of cDNA clones encoding the thymocyte antigens CD1a, b, c
demonstrates a hierarchy of exclusion in fibroblasts.";
J. Immunol. 143:1723-1730(1989).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.;
"Cloning of human full open reading frames in Gateway(TM) system entry
vector (pDONR201).";
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16710414; DOI=10.1038/nature04727;
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D.,
Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A.,
Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F.,
McDonald L., Evans R., Phillips K., Atkinson A., Cooper R., Jones C.,
Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P.,
Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K.,
Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G.,
Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D.,
Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G.,
Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J.,
Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R.,
Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D.,
Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G.,
Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M.,
Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J.,
Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M.,
Loveland J., Lovell J., Lush M.J., Lyne R., Martin S.,
Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S.,
Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C.,
Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z.,
Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E.,
Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A.,
Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R.,
Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V.,
Beck S., Rogers J., Bentley D.R.;
"The DNA sequence and biological annotation of human chromosome 1.";
Nature 441:315-321(2006).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 19-109.
PubMed=10488738; DOI=10.1034/j.1399-0039.1999.540202.x;
Han M., Hannick L.I., DiBrino M., Robinson M.A.;
"Polymorphism of human CD1 genes.";
Tissue Antigens 54:122-127(1999).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 204-296.
PubMed=3097645; DOI=10.1073/pnas.83.23.9154;
Martin L.H., Calabi F., Milstein C.;
"Isolation of CD1 genes: a family of major histocompatibility complex-
related differentiation antigens.";
Proc. Natl. Acad. Sci. U.S.A. 83:9154-9158(1986).
[8]
FUNCTION, INTERNALIZATION SIGNAL, AND SUBCELLULAR LOCATION.
PubMed=10899914; DOI=10.1084/jem.192.2.281;
Briken V., Jackman R.M., Watts G.F.M., Rogers R.A., Porcelli S.A.;
"Human CD1b and CD1c isoforms survey different intracellular
compartments for the presentation of microbial lipid antigens.";
J. Exp. Med. 192:281-288(2000).
[9]
FUNCTION.
PubMed=10786796; DOI=10.1038/35009119;
Moody D.B., Ulrichs T., Muehlecker W., Young D.C., Gurcha S.S.,
Grant E., Rosat J.-P., Brenner M.B., Costello C.E., Besra G.S.,
Porcelli S.A.;
"CD1c-mediated T-cell recognition of isoprenoid glycolipids in
Mycobacterium tuberculosis infection.";
Nature 404:884-888(2000).
[10]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=10890914; DOI=10.1073/pnas.150236797;
Sugita M., van Der Wel N., Rogers R.A., Peters P.J., Brenner M.B.;
"CD1c molecules broadly survey the endocytic system.";
Proc. Natl. Acad. Sci. U.S.A. 97:8445-8450(2000).
[11]
GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-38; ASN-75 AND ASN-78.
TISSUE=Leukemic T-cell;
PubMed=19349973; DOI=10.1038/nbt.1532;
Wollscheid B., Bausch-Fluck D., Henderson C., O'Brien R., Bibel M.,
Schiess R., Aebersold R., Watts J.D.;
"Mass-spectrometric identification and relative quantification of N-
linked cell surface glycoproteins.";
Nat. Biotechnol. 27:378-386(2009).
[12]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 19-201 IN COMPLEX WITH
MANNOSYL-BETA1-PHOSPHOMYCOKETIDE, FUNCTION, SUBUNIT, DISULFIDE BOND,
AND GLYCOSYLATION AT ASN-38.
PubMed=21167756; DOI=10.1016/j.immuni.2010.11.026;
Scharf L., Li N.S., Hawk A.J., Garzon D., Zhang T., Fox L.M.,
Kazen A.R., Shah S., Haddadian E.J., Gumperz J.E., Saghatelian A.,
Faraldo-Gomez J.D., Meredith S.C., Piccirilli J.A., Adams E.J.;
"The 2.5 a structure of CD1c in complex with a mycobacterial lipid
reveals an open groove ideally suited for diverse antigen
presentation.";
Immunity 33:853-862(2010).
-!- FUNCTION: Antigen-presenting protein that binds self and non-self
lipid and glycolipid antigens and presents them to T-cell
receptors on natural killer T-cells. {ECO:0000269|PubMed:10786796,
ECO:0000269|PubMed:10890914, ECO:0000269|PubMed:10899914,
ECO:0000269|PubMed:21167756}.
-!- SUBUNIT: Heterodimer with B2M (beta-2-microglobulin).
{ECO:0000269|PubMed:21167756}.
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:10890914,
ECO:0000269|PubMed:10899914}; Single-pass type I membrane protein
{ECO:0000255}. Endosome membrane {ECO:0000269|PubMed:10890914,
ECO:0000269|PubMed:3097645}; Single-pass type I membrane protein.
Lysosome {ECO:0000269|PubMed:10890914}. Note=Subject to
intracellular trafficking between the cell membrane and endosomes.
{ECO:0000269|PubMed:10890914, ECO:0000269|PubMed:3097645}.
-!- TISSUE SPECIFICITY: Expressed on cortical thymocytes, on certain
T-cell leukemias, and in various other tissues.
-!- MISCELLANEOUS: During protein synthesis and maturation, CD1 family
members bind endogenous lipids that are replaced by lipid or
glycolipid antigens when the proteins are internalized and pass
through endosomes or lysosomes, before trafficking back to the
cell surface.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; M22178; AAA51942.1; -; Genomic_DNA.
EMBL; M22174; AAA51942.1; JOINED; Genomic_DNA.
EMBL; M22175; AAA51942.1; JOINED; Genomic_DNA.
EMBL; M22176; AAA51942.1; JOINED; Genomic_DNA.
EMBL; M22177; AAA51942.1; JOINED; Genomic_DNA.
EMBL; M28827; AAA51941.1; -; mRNA.
EMBL; CR457080; CAG33361.1; -; mRNA.
EMBL; AL121986; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BC126465; AAI26466.1; -; mRNA.
EMBL; BC126467; AAI26468.1; -; mRNA.
EMBL; AF142667; AAD37580.1; -; Genomic_DNA.
EMBL; M14667; AAA51938.1; -; Genomic_DNA.
CCDS; CCDS1175.1; -.
PIR; C45801; HLHUCC.
RefSeq; NP_001756.2; NM_001765.2.
UniGene; Hs.132448; -.
PDB; 3OV6; X-ray; 2.50 A; A=19-201.
PDB; 4ONO; X-ray; 2.70 A; A=24-201.
PDB; 5C9J; X-ray; 2.40 A; A=24-203.
PDBsum; 3OV6; -.
PDBsum; 4ONO; -.
PDBsum; 5C9J; -.
ProteinModelPortal; P29017; -.
SMR; P29017; -.
IntAct; P29017; 2.
MINT; MINT-4656025; -.
STRING; 9606.ENSP00000357152; -.
iPTMnet; P29017; -.
PhosphoSitePlus; P29017; -.
SwissPalm; P29017; -.
BioMuta; CD1C; -.
DMDM; 143811371; -.
MaxQB; P29017; -.
PaxDb; P29017; -.
PeptideAtlas; P29017; -.
PRIDE; P29017; -.
DNASU; 911; -.
Ensembl; ENST00000368170; ENSP00000357152; ENSG00000158481.
GeneID; 911; -.
KEGG; hsa:911; -.
UCSC; uc001fru.4; human.
CTD; 911; -.
DisGeNET; 911; -.
EuPathDB; HostDB:ENSG00000158481.12; -.
GeneCards; CD1C; -.
HGNC; HGNC:1636; CD1C.
MIM; 188340; gene.
neXtProt; NX_P29017; -.
OpenTargets; ENSG00000158481; -.
PharmGKB; PA26195; -.
eggNOG; ENOG410JACG; Eukaryota.
eggNOG; ENOG41113WA; LUCA.
GeneTree; ENSGT00480000042665; -.
HOGENOM; HOG000111666; -.
HOVERGEN; HBG004453; -.
InParanoid; P29017; -.
KO; K06448; -.
OMA; ILYWGHH; -.
OrthoDB; EOG091G0H36; -.
PhylomeDB; P29017; -.
TreeFam; TF336723; -.
Reactome; R-HSA-198933; Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.
ChiTaRS; CD1C; human.
EvolutionaryTrace; P29017; -.
GenomeRNAi; 911; -.
PRO; PR:P29017; -.
Proteomes; UP000005640; Chromosome 1.
Bgee; ENSG00000158481; -.
CleanEx; HS_CD1C; -.
ExpressionAtlas; P29017; baseline and differential.
Genevisible; P29017; HS.
GO; GO:0010008; C:endosome membrane; IEA:UniProtKB-SubCell.
GO; GO:0005887; C:integral component of plasma membrane; TAS:ProtInc.
GO; GO:0005764; C:lysosome; IEA:UniProtKB-SubCell.
GO; GO:0005886; C:plasma membrane; TAS:Reactome.
GO; GO:0030881; F:beta-2-microglobulin binding; IBA:GO_Central.
GO; GO:0030883; F:endogenous lipid antigen binding; IDA:UniProtKB.
GO; GO:0030884; F:exogenous lipid antigen binding; IDA:UniProtKB.
GO; GO:0051861; F:glycolipid binding; IDA:UniProtKB.
GO; GO:0071723; F:lipopeptide binding; IDA:UniProtKB.
GO; GO:0002250; P:adaptive immune response; IEA:UniProtKB-KW.
GO; GO:0048007; P:antigen processing and presentation, exogenous lipid antigen via MHC class Ib; IBA:GO_Central.
GO; GO:0050776; P:regulation of immune response; TAS:Reactome.
GO; GO:0002286; P:T cell activation involved in immune response; IDA:UniProtKB.
Gene3D; 2.60.40.10; -; 1.
Gene3D; 3.30.500.10; -; 1.
InterPro; IPR007110; Ig-like_dom.
InterPro; IPR036179; Ig-like_dom_sf.
InterPro; IPR013783; Ig-like_fold.
InterPro; IPR003597; Ig_C1-set.
InterPro; IPR011161; MHC_I-like_Ag-recog.
InterPro; IPR037055; MHC_I-like_Ag-recog_sf.
InterPro; IPR011162; MHC_I/II-like_Ag-recog.
Pfam; PF07654; C1-set; 1.
Pfam; PF16497; MHC_I_3; 1.
SMART; SM00407; IGc1; 1.
SUPFAM; SSF48726; SSF48726; 1.
SUPFAM; SSF54452; SSF54452; 1.
PROSITE; PS50835; IG_LIKE; 1.
1: Evidence at protein level;
3D-structure; Adaptive immunity; Cell membrane; Complete proteome;
Disulfide bond; Endosome; Glycoprotein; Immunity;
Immunoglobulin domain; Lipid-binding; Lysosome; Membrane;
Polymorphism; Reference proteome; Signal; Transmembrane;
Transmembrane helix.
SIGNAL 1 17 {ECO:0000255}.
CHAIN 18 333 T-cell surface glycoprotein CD1c.
/FTId=PRO_0000014580.
TOPO_DOM 18 302 Extracellular. {ECO:0000255}.
TRANSMEM 303 323 Helical. {ECO:0000255}.
TOPO_DOM 324 333 Cytoplasmic. {ECO:0000255}.
DOMAIN 206 296 Ig-like.
MOTIF 329 332 Internalization signal.
CARBOHYD 38 38 N-linked (GlcNAc...) asparagine.
{ECO:0000269|PubMed:19349973,
ECO:0000269|PubMed:21167756}.
CARBOHYD 70 70 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 75 75 N-linked (GlcNAc...) asparagine.
{ECO:0000269|PubMed:19349973}.
CARBOHYD 78 78 N-linked (GlcNAc...) asparagine;
atypical. {ECO:0000269|PubMed:19349973}.
CARBOHYD 146 146 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
DISULFID 120 185 {ECO:0000255|PROSITE-ProRule:PRU00114,
ECO:0000269|PubMed:21167756}.
DISULFID 225 280 {ECO:0000255|PROSITE-ProRule:PRU00114}.
VARIANT 70 70 N -> T (in dbSNP:rs3138100).
/FTId=VAR_031564.
VARIANT 300 300 F -> S (in dbSNP:rs3138105).
{ECO:0000269|PubMed:2701945}.
/FTId=VAR_031565.
CONFLICT 290 290 Q -> R (in Ref. 3; CAG33361).
{ECO:0000305}.
CONFLICT 327 333 CSYQDIL -> W (in Ref. 1; AAA51942).
{ECO:0000305}.
STRAND 25 38 {ECO:0000244|PDB:5C9J}.
STRAND 41 50 {ECO:0000244|PDB:5C9J}.
STRAND 53 59 {ECO:0000244|PDB:5C9J}.
TURN 60 63 {ECO:0000244|PDB:5C9J}.
STRAND 64 67 {ECO:0000244|PDB:5C9J}.
TURN 70 75 {ECO:0000244|PDB:5C9J}.
HELIX 78 103 {ECO:0000244|PDB:5C9J}.
HELIX 107 109 {ECO:0000244|PDB:5C9J}.
STRAND 111 123 {ECO:0000244|PDB:5C9J}.
STRAND 129 136 {ECO:0000244|PDB:5C9J}.
STRAND 139 144 {ECO:0000244|PDB:5C9J}.
STRAND 146 151 {ECO:0000244|PDB:5C9J}.
HELIX 157 168 {ECO:0000244|PDB:5C9J}.
HELIX 171 182 {ECO:0000244|PDB:5C9J}.
HELIX 184 200 {ECO:0000244|PDB:5C9J}.
SEQUENCE 333 AA; 37654 MW; 8E4E057097E3E440 CRC64;
MLFLQFLLLA LLLPGGDNAD ASQEHVSFHV IQIFSFVNQS WARGQGSGWL DELQTHGWDS
ESGTIIFLHN WSKGNFSNEE LSDLELLFRF YLFGLTREIQ DHASQDYSKY PFEVQVKAGC
ELHSGKSPEG FFQVAFNGLD LLSFQNTTWV PSPGCGSLAQ SVCHLLNHQY EGVTETVYNL
IRSTCPRFLL GLLDAGKMYV HRQVRPEAWL SSRPSLGSGQ LLLVCHASGF YPKPVWVTWM
RNEQEQLGTK HGDILPNADG TWYLQVILEV ASEEPAGLSC RVRHSSLGGQ DIILYWGHHF
SMNWIALVVI VPLVILIVLV LWFKKHCSYQ DIL


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