P29017 (CD1C_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
T-cell surface glycoprotein CD1c

Alternative name(s):
CD_antigen=CD1c

Gene names

Name:

CD1C

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	333 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.8 Ref.9 Ref.10 Ref.12
Subunit structure	Heterodimer with B2M (beta-2-microglobulin). Ref.12
Subcellular location	Cell membrane; Single-pass type I membrane protein. Endosome membrane. Note: Subject to intracellular trafficking between the cell membrane and endosomes. Ref.8 Ref.10
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.
Sequence similarities	Contains 1 Ig-like (immunoglobulin-like) domain.

Ontologies

Keywords
Biological process	Adaptive immunity Immunity
Cellular component	Cell membrane Endosome Membrane
Coding sequence diversity	Polymorphism
Domain	Immunoglobulin domain Signal Transmembrane Transmembrane helix
Ligand	Lipid-binding
PTM	Disulfide bond Glycoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	T cell activation involved in immune response Inferred from direct assay Ref.12. Source: UniProtKB antigen processing and presentation Inferred from electronic annotation. Source: InterPro
Cellular_component	endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell integral to plasma membrane Traceable author statement PubMed 1702817. Source: ProtInc
Molecular_function	endogenous lipid antigen binding Inferred from direct assay Ref.12. Source: UniProtKB exogenous lipid antigen binding Inferred from direct assay Ref.12. Source: UniProtKB glycolipid binding Inferred from direct assay Ref.12. Source: UniProtKB lipopeptide binding Inferred from direct assay Ref.12. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 17

17

Potential

Chain

18 – 333

316

T-cell surface glycoprotein CD1c

PRO_0000014580

Regions

Topological domain

18 – 302

285

Extracellular Potential

Transmembrane

303 – 323

21

Helical; Potential

Topological domain

324 – 333

10

Cytoplasmic Potential

Domain

206 – 296

91

Ig-like

Motif

329 – 332

4

Internalization signal

Amino acid modifications

Glycosylation

38

1

N-linked (GlcNAc...) Ref.11 Ref.12

Glycosylation

70

1

N-linked (GlcNAc...) Potential

Glycosylation

75

1

N-linked (GlcNAc...) Ref.11

Glycosylation

78

1

N-linked (GlcNAc...) Ref.11

Glycosylation

146

1

N-linked (GlcNAc...) Potential

Disulfide bond

120 ↔ 185

Ref.12

Disulfide bond

225 ↔ 280

By similarity

Natural variations

Natural variant

70

1

N → T.
Corresponds to variant rs3138100 [ dbSNP | Ensembl ].

VAR_031564

Natural variant

300

1

F → S. Ref.2
Corresponds to variant rs3138105 [ dbSNP | Ensembl ].

VAR_031565

Experimental info

Sequence conflict

290

1

Q → R in CAG33361. Ref.3

Sequence conflict

327 – 333

7

CSYQDIL → W in AAA51942. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

333

Helix Strand Turn

Details...

Beta strand

25 – 40

16

Helix

78 – 92

15

Helix

96 – 100

5

Beta strand

112 – 118

7

Beta strand

120 – 123

4

Beta strand

133 – 136

4

Beta strand

140 – 145

6

Beta strand

148 – 151

4

Helix

159 – 168

10

Helix

174 – 182

9

Helix

184 – 189

6

Sequences

	Sequence		Length	Mass (Da)
	P29017 [UniParc]. Last modified April 3, 2007. Version 2. Checksum: 8E4E057097E3E440	FASTA	333	37,654
	10 20 30 40 50 60 MLFLQFLLLA LLLPGGDNAD ASQEHVSFHV IQIFSFVNQS WARGQGSGWL DELQTHGWDS 70 80 90 100 110 120 ESGTIIFLHN WSKGNFSNEE LSDLELLFRF YLFGLTREIQ DHASQDYSKY PFEVQVKAGC 130 140 150 160 170 180 ELHSGKSPEG FFQVAFNGLD LLSFQNTTWV PSPGCGSLAQ SVCHLLNHQY EGVTETVYNL 190 200 210 220 230 240 IRSTCPRFLL GLLDAGKMYV HRQVRPEAWL SSRPSLGSGQ LLLVCHASGF YPKPVWVTWM 250 260 270 280 290 300 RNEQEQLGTK HGDILPNADG TWYLQVILEV ASEEPAGLSC RVRHSSLGGQ DIILYWGHHF 310 320 330 SMNWIALVVI VPLVILIVLV LWFKKHCSYQ DIL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure and expression of the human thymocyte antigens CD1a, CD1b, and CD1c." Martin L.H., Calabi F., Lefebvre F.-A., Bilsland C.A.G., Milstein C. Proc. Natl. Acad. Sci. U.S.A. 84:9189-9193(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Expression of cDNA clones encoding the thymocyte antigens CD1a, b, c demonstrates a hierarchy of exclusion in fibroblasts." Aruffo A., Seed B. J. Immunol. 143:1723-1730(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT SER-300.
[3]	"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)." Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B. Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]	"The DNA sequence and biological annotation of human chromosome 1." 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. Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]	"Polymorphism of human CD1 genes." Han M., Hannick L.I., DiBrino M., Robinson M.A. Tissue Antigens 54:122-127(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 19-109.
[7]	"Isolation of CD1 genes: a family of major histocompatibility complex-related differentiation antigens." Martin L.H., Calabi F., Milstein C. Proc. Natl. Acad. Sci. U.S.A. 83:9154-9158(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 204-296.
[8]	"Human CD1b and CD1c isoforms survey different intracellular compartments for the presentation of microbial lipid antigens." Briken V., Jackman R.M., Watts G.F.M., Rogers R.A., Porcelli S.A. J. Exp. Med. 192:281-288(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERNALIZATION SIGNAL, SUBCELLULAR LOCATION.
[9]	"CD1c-mediated T-cell recognition of isoprenoid glycolipids in Mycobacterium tuberculosis infection." 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. Nature 404:884-888(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[10]	"CD1c molecules broadly survey the endocytic system." Sugita M., van Der Wel N., Rogers R.A., Peters P.J., Brenner M.B. Proc. Natl. Acad. Sci. U.S.A. 97:8445-8450(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[11]	"Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins." Wollscheid B., Bausch-Fluck D., Henderson C., O'Brien R., Bibel M., Schiess R., Aebersold R., Watts J.D. Nat. Biotechnol. 27:378-386(2009) [PubMed] [Europe PMC] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-38; ASN-75 AND ASN-78, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[12]	"The 2.5 a structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation." 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. Immunity 33:853-862(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 19-201 IN COMPLEX WITH MANNOSYL-BETA1-PHOSPHOMYCOKETIDE, FUNCTION, SUBUNIT, DISULFIDE BOND, GLYCOSYLATION AT ASN-38.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M22178 , M22174, M22175, M22176, M22177 Genomic DNA. Translation: AAA51942.1.
M28827 mRNA. Translation: AAA51941.1.
CR457080 mRNA. Translation: CAG33361.1.
AL121986 Genomic DNA. Translation: CAI10850.1.
BC126465 mRNA. Translation: AAI26466.1.
BC126467 mRNA. Translation: AAI26468.1.
AF142667 Genomic DNA. Translation: AAD37580.1.
M14667 Genomic DNA. Translation: AAA51938.1.

IPI

IPI00019850.

PIR

HLHUCC. C45801.

RefSeq

NP_001756.2. NM_001765.2.

UniGene

Hs.132448.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3OV6	X-ray	2.50	A	19-201	[»]

ProteinModelPortal

P29017.

ModBase

Search...

Protein-protein interaction databases

IntAct

P29017. 2 interactions.

STRING

9606.ENSP00000357152.

Polymorphism databases

DMDM

143811371.

Proteomic databases

PaxDb

P29017.

PRIDE

P29017.

Protocols and materials databases

DNASU

911.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000368170; ENSP00000357152; ENSG00000158481.

GeneID

911.

KEGG

hsa:911.

UCSC

uc001fru.3. human.

Organism-specific databases

CTD

911.

GeneCards

GC01P158259.

HGNC

HGNC:1636. CD1C.

MIM

188340. gene.

neXtProt

NX_P29017.

PharmGKB

PA26195.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG319535.

HOGENOM

HOG000111666.

HOVERGEN

HBG004453.

KO

K06448.

OrthoDB

EOG40ZQZZ.

PhylomeDB

P29017.

Gene expression databases

ArrayExpress

P29017.

Bgee

P29017.

CleanEx

HS_CD1C.

Genevestigator

P29017.

GermOnline

ENSG00000158481. Homo sapiens.

Family and domain databases

Gene3D

2.60.40.10. 1 hit.
3.30.500.10. 1 hit.

InterPro

IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003597. Ig_C1-set.
IPR011161. MHC_I-like_Ag-recog.
IPR011162. MHC_I/II-like_Ag-recog.
[Graphical view]

Pfam

PF07654. C1-set. 1 hit.
[Graphical view]

SMART

SM00407. IGc1. 1 hit.
[Graphical view]

SUPFAM

SSF54452. MHC_I/II-like_Ag-recog. 1 hit.

PROSITE

PS50835. IG_LIKE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P29017.

GenomeRNAi

911.

NextBio

3758.

SOURCE

Search...

Entry information

Entry name

CD1C_HUMAN

Accession

Primary (citable) accession number: P29017
Secondary accession number(s): Q5TDJ7 , Q6IAS4, Q9UMM0, Q9UN96

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	April 3, 2007
Last modified:	May 1, 2013
This is version 121 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.