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P11609 (CD1D1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 144. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Antigen-presenting glycoprotein CD1d1
Alternative name(s):
CD_antigen=CD1d.1
Gene names
Name:Cd1d1
Synonyms:Cd1.1
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length336 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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 processImmunity
Innate immunity
   Cellular componentCell membrane
Endosome
Lysosome
Membrane
   DomainImmunoglobulin domain
Signal
Transmembrane
Transmembrane helix
   PTMDisulfide bond
Glycoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processantigen processing and presentation

Inferred from direct assay Ref.4. Source: MGI

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

regulation of immune response

Inferred from mutant phenotype PubMed 9133426. Source: MGI

   Cellular_componentearly 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 component of 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_functionT cell receptor binding

Inferred from direct assay PubMed 22065767. Source: MGI

beta-2-microglobulin binding

Inferred from Biological aspect of Ancestor. Source: RefGenome

endogenous lipid antigen binding

Inferred from direct assay PubMed 14722359. Source: MGI

exogenous lipid antigen binding

Inferred from Biological aspect of Ancestor. Source: RefGenome

lipopeptide binding

Inferred from Biological aspect of Ancestor. Source: RefGenome

protein binding

Inferred from physical interaction Ref.4. Source: MGI

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2121 Potential
Chain22 – 336315Antigen-presenting glycoprotein CD1d1
PRO_0000014591

Regions

Topological domain22 – 305284Extracellular Potential
Transmembrane306 – 32621Helical; Potential
Topological domain327 – 33610Cytoplasmic Potential
Domain207 – 29791Ig-like
Motif332 – 3354Internalization signal

Sites

Binding site981Glycolipid
Binding site1711Glycolipid
Binding site1741Glycolipid

Amino acid modifications

Glycosylation251N-linked (GlcNAc...) Potential
Glycosylation381N-linked (GlcNAc...) Ref.7 Ref.8 Ref.9
Glycosylation601N-linked (GlcNAc...) Ref.7 Ref.8 Ref.9
Glycosylation1281N-linked (GlcNAc...) Potential
Glycosylation1831N-linked (GlcNAc...) Ref.7 Ref.8 Ref.9
Disulfide bond122 ↔ 186 Ref.5 Ref.7 Ref.8 Ref.9
Disulfide bond226 ↔ 281 Ref.5 Ref.7 Ref.8 Ref.9

Experimental info

Sequence conflict2191D → H in BAB22206. Ref.2
Sequence conflict2191D → H in CAA31568. Ref.3
Sequence conflict2401W → C in AAA37391. Ref.1

Secondary structure

.................................................... 336
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P11609 [UniParc].

Last modified December 15, 1998. Version 3.
Checksum: E4A666E1942E0114

FASTA33638,554
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M63695 mRNA. Translation: AAA37391.1.
AK002582 mRNA. Translation: BAB22206.1.
X13170 Genomic DNA. Translation: CAA31568.1.
CCDSCCDS17449.1.
PIRI49581.
S01297.
RefSeqNP_031665.2. NM_007639.3.
UniGeneMm.1894.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1CD1X-ray2.67A/C22-336[»]
1Z5LX-ray2.20A/C19-297[»]
1ZHNX-ray2.80A25-297[»]
2AKRX-ray1.90A/C19-297[»]
2FIKX-ray1.80A19-297[»]
2GAZX-ray2.61A19-297[»]
2Q7YX-ray1.95A/C19-297[»]
3ARBX-ray2.70A19-297[»]
3ARDX-ray3.01A19-297[»]
3AREX-ray2.80A19-297[»]
3ARFX-ray2.90A19-297[»]
3ARGX-ray3.00A19-297[»]
3AU1X-ray2.50A19-297[»]
3G08X-ray1.60A19-297[»]
3GMLX-ray1.70A19-297[»]
3GMMX-ray1.80A19-297[»]
3GMNX-ray1.70A19-297[»]
3GMOX-ray1.60A19-297[»]
3GMPX-ray1.70A19-297[»]
3GMQX-ray1.80A19-297[»]
3GMRX-ray1.90A19-297[»]
3HE6X-ray2.90A19-297[»]
3HE7X-ray2.80A19-297[»]
3ILPX-ray1.85A19-297[»]
3ILQX-ray2.05C19-297[»]
3MA7X-ray2.29A/C19-297[»]
3O8XX-ray2.74A19-297[»]
3O9WX-ray2.80A19-297[»]
3QI9X-ray2.30A19-297[»]
3QUXX-ray2.91A19-297[»]
3QUYX-ray2.25A19-297[»]
3QUZX-ray2.30A19-297[»]
3RTQX-ray2.80A19-297[»]
3RUGX-ray2.20A/C19-297[»]
3RZCX-ray2.80A19-297[»]
3SCMX-ray2.50A19-297[»]
3SDAX-ray2.80A19-297[»]
3SDCX-ray3.10A19-297[»]
3SDDX-ray3.00A19-297[»]
3T1FX-ray1.70A19-297[»]
3TA3X-ray2.70A19-297[»]
3TN0X-ray3.20A19-297[»]
3TO4X-ray3.10A19-297[»]
3TVMX-ray2.80A/E19-297[»]
3UBXX-ray3.10A/D19-297[»]
4APQX-ray3.00A19-297[»]
4EI5X-ray3.10A/E19-297[»]
4ELMX-ray3.48A/C19-297[»]
4IRJX-ray3.00A19-297[»]
4IRSX-ray2.80A19-297[»]
ProteinModelPortalP11609.
SMRP11609. Positions 25-297.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-6127N.
IntActP11609. 1 interaction.
MINTMINT-1864400.

PTM databases

PhosphoSiteP11609.

Proteomic databases

PaxDbP11609.
PRIDEP11609.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000029717; ENSMUSP00000029717; ENSMUSG00000028076.
GeneID12479.
KEGGmmu:12479.
UCSCuc012cre.1. mouse.

Organism-specific databases

CTD12479.
MGIMGI:107674. Cd1d1.

Phylogenomic databases

eggNOGNOG26626.
GeneTreeENSGT00480000042665.
HOGENOMHOG000111666.
HOVERGENHBG004453.
InParanoidP11609.
KOK06448.
OrthoDBEOG7DZ8K9.
PhylomeDBP11609.
TreeFamTF336723.

Gene expression databases

ArrayExpressP11609.
BgeeP11609.
CleanExMM_CD1D1.
GenevestigatorP11609.

Family and domain databases

Gene3D2.60.40.10. 1 hit.
3.30.500.10. 1 hit.
InterProIPR007110. 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]
PfamPF07654. C1-set. 1 hit.
[Graphical view]
SMARTSM00407. IGc1. 1 hit.
[Graphical view]
SUPFAMSSF54452. SSF54452. 1 hit.
PROSITEPS50835. IG_LIKE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP11609.
NextBio281370.
PROP11609.
SOURCESearch...

Entry information

Entry nameCD1D1_MOUSE
AccessionPrimary (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: July 9, 2014
This is version 144 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot