P11609 (CD1D1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Antigen-presenting glycoprotein CD1d1

Alternative name(s):
CD_antigen=CD1d.1

Gene names

Name:	Cd1d1
Synonyms:	Cd1.1

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	336 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 glycolipids and presents them to T-cell receptors on natural killer T-cells. Ref.4 Ref.6 Ref.8
Subunit structure	Heterodimer with B2M (beta-2-microglobulin). Interacts with MHC II and CD74. Ref.4
Subcellular location	Cell membrane; Single-pass type I membrane protein. Endosome membrane. Lysosome membrane. Note: Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes. Ref.4
Tissue specificity	Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues.
Post-translational modification	N-glycosylated. Ref.4 Ref.6 Ref.7 Ref.8 Ref.9
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, before trafficking back to the cell surface.
Sequence similarities	Contains 1 Ig-like (immunoglobulin-like) domain.

Ontologies

Keywords
Biological process	Immunity Innate immunity
Cellular component	Cell membrane Endosome Lysosome Membrane
Domain	Immunoglobulin domain Signal Transmembrane Transmembrane helix
PTM	Disulfide bond Glycoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	antigen processing and presentation, exogenous lipid antigen via MHC class Ib Inferred from direct assay PubMed 14557411. Source: MGI innate immune response Inferred from electronic annotation. Source: UniProtKB-KW positive regulation of NK T cell activation Inferred from direct assay PubMed 10201995Ref.4PubMed 7538697. Source: MGI positive regulation of NK T cell differentiation Inferred from mutant phenotype PubMed 10201995PubMed 9133426. Source: MGI positive regulation of T cell mediated cytotoxicity Inferred from direct assay PubMed 10201995. Source: MGI positive regulation of interferon-gamma biosynthetic process Inferred from mutant phenotype PubMed 9133426. Source: MGI positive regulation of interleukin-2 biosynthetic process Inferred from direct assay PubMed 10201995Ref.4PubMed 14557411PubMed 7538697. Source: MGI positive regulation of interleukin-4 biosynthetic process Inferred from direct assay Ref.4PubMed 7538697. Source: MGI positive regulation of macrophage activation Inferred from direct assay PubMed 21460847. Source: MGI positive thymic T cell selection Inferred from mutant phenotype PubMed 9133426. Source: MGI
Cellular_component	early endosome Inferred from direct assay Ref.4. Source: MGI endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell external side of plasma membrane Inferred from direct assay PubMed 10201995Ref.4PubMed 14557411PubMed 17082577PubMed 9133426. Source: MGI integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW late endosome Inferred from direct assay Ref.4. Source: MGI lysosomal membrane Inferred from electronic annotation. Source: UniProtKB-SubCell lysosome Inferred from direct assay Ref.4PubMed 14557411. Source: MGI
Molecular_function	T cell receptor binding Inferred from direct assay PubMed 22065767. Source: MGI endogenous lipid antigen binding Inferred from direct assay PubMed 14722359. Source: MGI
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 21

21

Chain

22 – 336

315

Antigen-presenting glycoprotein CD1d1

PRO_0000014591

Regions

Topological domain

22 – 305

284

Extracellular Potential

Transmembrane

306 – 326

21

Helical; Potential

Topological domain

327 – 336

10

Cytoplasmic Potential

Domain

207 – 297

91

Ig-like

Motif

332 – 335

4

Internalization signal

Sites

Binding site

98

1

Glycolipid

Binding site

171

1

Glycolipid

Binding site

174

1

Glycolipid

Amino acid modifications

Glycosylation

25

1

N-linked (GlcNAc...) Potential

Glycosylation

38

1

N-linked (GlcNAc...) Ref.7 Ref.8 Ref.9

Glycosylation

60

1

N-linked (GlcNAc...) Ref.7 Ref.8 Ref.9

Glycosylation

128

1

N-linked (GlcNAc...) Potential

Glycosylation

183

1

N-linked (GlcNAc...) Ref.7 Ref.8 Ref.9

Disulfide bond

122 ↔ 186

Ref.5 Ref.7 Ref.8 Ref.9

Disulfide bond

226 ↔ 281

Ref.5 Ref.7 Ref.8 Ref.9

Experimental info

Sequence conflict

219

1

D → H in BAB22206. Ref.2

Sequence conflict

219

1

D → H in CAA31568. Ref.3

Sequence conflict

240

1

W → C in AAA37391. Ref.1

Secondary structure

1

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336

Helix Strand Turn

Details...

Beta strand

26 – 38

13

Beta strand

41 – 50

10

Beta strand

53 – 58

6

Beta strand

66 – 69

4

Turn

70 – 75

6

Helix

78 – 105

28

Turn

107 – 109

3

Beta strand

112 – 124

13

Beta strand

126 – 128

3

Beta strand

130 – 138

9

Beta strand

141 – 147

7

Beta strand

150 – 153

4

Helix

159 – 161

3

Helix

162 – 170

9

Helix

172 – 183

12

Helix

185 – 196

12

Helix

198 – 201

4

Beta strand

208 – 214

7

Beta strand

217 – 220

4

Beta strand

222 – 234

13

Beta strand

237 – 242

6

Beta strand

250 – 252

3

Beta strand

263 – 271

9

Turn

273 – 278

6

Beta strand

279 – 284

6

Helix

286 – 288

3

Beta strand

293 – 296

4

Sequences

	Sequence		Length	Mass (Da)
	P11609 [UniParc]. Last modified December 15, 1998. Version 3. Checksum: E4A666E1942E0114	FASTA	336	38,554
	10 20 30 40 50 60 MRYLPWLLLW AFLQVWGQSE AQQKNYTFRC LQMSSFANRS WSRTDSVVWL GDLQTHRWSN 70 80 90 100 110 120 DSATISFTKP WSQGKLSNQQ WEKLQHMFQV YRVSFTRDIQ ELVKMMSPKE DYPIEIQLSA 130 140 150 160 170 180 GCEMYPGNAS ESFLHVAFQG KYVVRFWGTS WQTVPGAPSW LDLPIKVLNA DQGTSATVQM 190 200 210 220 230 240 LLNDTCPLFV RGLLEAGKSD LEKQEKPVAW LSSVPSSADG HRQLVCHVSG FYPKPVWVMW 250 260 270 280 290 300 MRGDQEQQGT HRGDFLPNAD ETWYLQATLD VEAGEEAGLA CRVKHSSLGG QDIILYWDAR 310 320 330 QAPVGLIVFI VLIMLVVVGA VVYYIWRRRS AYQDIR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Isolation and expression of cDNA encoding the murine homologues of CD1." Balk S.P., Bleicher P.A., Terhorst C. J. Immunol. 146:768-774(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: C57BL/6J. Tissue: Kidney.
[3]	"Mouse CD1 is distinct from and co-exists with TL in the same thymus." Bradbury A., Belt K.T., Neri T.M., Milstein C., Calabi F. EMBO J. 7:3081-3086(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-297. Tissue: Thymus.
[4]	"CD1d endosomal trafficking is independently regulated by an intrinsic CD1d-encoded tyrosine motif and by the invariant chain." Jayawardena-Wolf J., Benlagha K., Chiu Y.-H., Mehr R., Bendelac A. Immunity 15:897-908(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH CD74, GLYCOSYLATION.
[5]	"Crystal structure of mouse CD1: an MHC-like fold with a large hydrophobic binding groove." Zeng Z., Castano A.R., Segelke B.W., Stura E.A., Peterson P.A., Wilson I.A. Science 277:339-345(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.67 ANGSTROMS) OF 25-297 IN COMPLEX WITH B2M, DISULFIDE BONDS.
[6]	"Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity." Zajonc D.M., Maricic I., Wu D., Halder R., Roy K., Wong C.-H., Kumar V., Wilson I.A. J. Exp. Med. 202:1517-1526(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 19-297 IN COMPLEX WITH B2M AND CIS-TETRACOSENOYL SULFATIDE, FUNCTION, GLYCOSYLATION.
[7]	"Crystal structure of mouse CD1d bound to the self ligand phosphatidylcholine: a molecular basis for NKT cell activation." Giabbai B., Sidobre S., Crispin M.D.M., Sanchez-Ruiz Y., Bachi A., Kronenberg M., Wilson I.A., Degano M. J. Immunol. 175:977-984(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 25-297 IN COMPLEX WITH PHOSPHATIDYLCHOLINE AND B2M, GLYCOSYLATION AT ASN-38; ASN-60 AND ASN-183, DISULFIDE BONDS.
[8]	"Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor." Zajonc D.M., Cantu C. III, Mattner J., Zhou D., Savage P.B., Bendelac A., Wilson I.A., Teyton L. Nat. Immunol. 6:810-818(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 19-297 IN COMPLEX WITH GALACTOSYLCERAMIDE AND B2M, FUNCTION, GLYCOSYLATION AT ASN-38; ASN-60 AND ASN-183, DISULFIDE BONDS.
[9]	"Design of natural killer T cell activators: structure and function of a microbial glycosphingolipid bound to mouse CD1d." Wu D., Zajonc D.M., Fujio M., Sullivan B.A., Kinjo Y., Kronenberg M., Wilson I.A., Wong C.-H. Proc. Natl. Acad. Sci. U.S.A. 103:3972-3977(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 19-297 IN COMPLEX WITH GLYCOSPHINGOLIPID AND B2M, GLYCOSYLATION AT ASN-38; ASN-60 AND ASN-183, DISULFIDE BONDS.
+	Additional computationally mapped references.

Web resources

Functional Glycomics Gateway - Glycan Binding

CD1d1

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M63695 mRNA. Translation: AAA37391.1.
AK002582 mRNA. Translation: BAB22206.1.
X13170 Genomic DNA. Translation: CAA31568.1.

IPI

IPI00320065.

PIR

I49581.
S01297.

RefSeq

NP_031665.2. NM_007639.3.

UniGene

Mm.1894.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CD1	X-ray	2.67	A/C	22-336	[»]
1Z5L	X-ray	2.20	A/C	19-297	[»]
1ZHN	X-ray	2.80	A	25-297	[»]
2AKR	X-ray	1.90	A/C	19-297	[»]
2FIK	X-ray	1.80	A	19-297	[»]
2GAZ	X-ray	2.61	A	19-297	[»]
2Q7Y	X-ray	1.95	A/C	19-297	[»]
3ARB	X-ray	2.70	A	19-297	[»]
3ARD	X-ray	3.01	A	19-297	[»]
3ARE	X-ray	2.80	A	19-297	[»]
3ARF	X-ray	2.90	A	19-297	[»]
3ARG	X-ray	3.00	A	19-297	[»]
3AU1	X-ray	2.50	A	19-297	[»]
3G08	X-ray	1.60	A	19-297	[»]
3GML	X-ray	1.70	A	19-297	[»]
3GMM	X-ray	1.80	A	19-297	[»]
3GMN	X-ray	1.70	A	19-297	[»]
3GMO	X-ray	1.60	A	19-297	[»]
3GMP	X-ray	1.70	A	19-297	[»]
3GMQ	X-ray	1.80	A	19-297	[»]
3GMR	X-ray	1.90	A	19-297	[»]
3HE6	X-ray	2.90	A	19-297	[»]
3HE7	X-ray	2.80	A	19-297	[»]
3ILP	X-ray	1.85	A	19-297	[»]
3ILQ	X-ray	2.05	C	19-297	[»]
3MA7	X-ray	2.29	A/C	19-297	[»]
3O8X	X-ray	2.74	A	19-297	[»]
3O9W	X-ray	2.80	A	19-297	[»]
3QI9	X-ray	2.30	A	19-297	[»]
3QUX	X-ray	2.91	A	19-297	[»]
3QUY	X-ray	2.25	A	19-297	[»]
3QUZ	X-ray	2.30	A	19-297	[»]
3RUG	X-ray	2.20	A/C	19-297	[»]
3RZC	X-ray	2.80	A	19-297	[»]
3SCM	X-ray	2.50	A	19-297	[»]
3SDA	X-ray	2.80	A	19-297	[»]
3SDC	X-ray	3.10	A	19-297	[»]
3SDD	X-ray	3.00	A	19-297	[»]
3T1F	X-ray	1.70	A	19-297	[»]
3TA3	X-ray	2.70	A	19-297	[»]
3TN0	X-ray	3.20	A	19-297	[»]
3TO4	X-ray	3.10	A	19-297	[»]
3TVM	X-ray	2.80	A/E	19-297	[»]
3UBX	X-ray	3.10	A/D	19-297	[»]
4EI5	X-ray	3.10	A/E	19-297	[»]
4ELM	X-ray	3.48	A/C	19-297	[»]

ProteinModelPortal

P11609.

SMR

P11609. Positions 25-297.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6127N.

IntAct

P11609. 1 interaction.

PTM databases

PhosphoSite

P11609.

Proteomic databases

PaxDb

P11609.

PRIDE

P11609.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000029717; ENSMUSP00000029717; ENSMUSG00000028076.

GeneID

12479.

KEGG

mmu:12479.

UCSC

uc008prs.1. mouse.

Organism-specific databases

CTD

12479.

MGI

MGI:107674. Cd1d1.

Phylogenomic databases

eggNOG

NOG26626.

GeneTree

ENSGT00480000042665.

HOGENOM

HOG000111666.

HOVERGEN

HBG004453.

InParanoid

P11609.

KO

K06448.

OrthoDB

EOG40ZQZZ.

Gene expression databases

ArrayExpress

P11609.

Bgee

P11609.

CleanEx

MM_CD1D1.

Genevestigator

P11609.

GermOnline

ENSMUSG00000028076. Mus musculus.

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

P11609.

NextBio

281370.

SOURCE

Search...

Entry information

Entry name

CD1D1_MOUSE

Accession

Primary (citable) accession number: P11609
Secondary accession number(s): Q91XK9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	December 15, 1998
Last modified:	April 3, 2013
This is version 133 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program