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The crystal structure of human CD1d with and without alpha-Galactosylceramide
Biology and Chemistry Report
1ZT4
  •   Structure Details   Hide

    Structure Keywords

    Keywords IMMUNE SYSTEM
    Text human CD1d, CD1, MHC class I, empty binding groove, glycolipid, alpha-galactosylceramide, alpha-GalCer, Structural Proteomics in Europe, SPINE, Structural Genomics, IMMUNE SYSTEM

    Polymeric Molecules

    Chain A,C
    Description T-cell surface glycoprotein CD1d 
    Fragment CD1d heavy chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 31819.1 
    Source Method genetically manipulated  
    Entity Name CD1d antigen, R3G1 
    Chain B,D
    Description Beta-2-microglobulin 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11879.5 
    Source Method genetically manipulated  
    Entity Name HDCMA22P 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    AGH  N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE  C50 H99 N O9   858.32  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C CD1D_HUMAN D3DVD5     
    B,D B2MG_HUMAN P61769     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 130694    
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain B,D
    GO ID   Ontology GO Term Definition
    2376   Immune System Process  Any Process Involved in the Development or Functioning of the Immune System an Organismal System For Calibrated Responses to Potential Internal or Invasive Threats. 
    2474   Antigen Processing and Presentation of Peptide Antigen Via Mhc Class I  The Process in Which an Antigen Presenting Cell Expresses a Peptide Antigen On Its Cell Surface in Association with an Mhc Class I Protein Complex. Class I Here Refers to Classical Class I Molecules. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    42612   Mhc Class I Protein Complex  A Transmembrane Protein Complex Composed of a Mhc Class I Alpha Chain and an Invariant Beta2 Microglobin Chain and with or Without a Bound Peptide Antigen. Class I Here Refers to Classical Class I Molecules. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    42802   Identical Protein Binding  Interacting Selectively and Non Covalently with an Identical Protein or Proteins. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B,D
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene b2m
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Hms174
    Host Vector Type Plasmid
    Host Plasmid Name pET23d


    Chain A,C
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene cd1d
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Hms174
    Host Vector Type Plasmid
    Host Plasmid Name pET23d


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1q23.1 912     CD1d molecule CD1D    
    15 15q21-q22.2 567     beta-2-microglobulin B2M    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs145764530 LS-SNP   dbSNP   A 20 N - > K Beta Ladder 1% (Buried) 1 158151297
    rs150689409 LS-SNP   dbSNP   A 23 W - > S Beta Ladder 26% (Intermediate) 1 158151305
    rs147976430 LS-SNP   dbSNP   A 31 W - > R Beta Ladder 15% (Intermediate) 1 158151328
    rs150540703 LS-SNP   dbSNP   A 37 T - > M Beta Ladder 0% (Buried) 1 158151347
    rs62621276 LS-SNP   dbSNP   A 46 T - > S Bend 42% (Exposed) 1 158151373
    rs139809600 LS-SNP   dbSNP   A 48 R - > C Beta Ladder 56% (Exposed) 1 158151379
    rs200638686 LS-SNP   dbSNP   A 82 K - > M Helix 29% (Intermediate) 1 158151482
    rs145209409 LS-SNP   dbSNP   A 90 L - > V Coil 21% (Intermediate) 1 158151505 AGH
    rs199803276 LS-SNP   dbSNP   A 94 L - > S Beta Ladder 3% (Buried) 1 158151828 AGH
    rs142254126 LS-SNP   dbSNP   A 100 A - > S Beta Ladder 14% (Intermediate) 1 158151845 AGH
    rs141459313 LS-SNP   dbSNP   A 127 Q - > P Beta Ladder 54% (Exposed) 1 158151927 AGH
    rs150267466 LS-SNP   dbSNP   A 132 E - > G Beta Ladder 44% (Exposed) 1 158151942
    rs112389115 LS-SNP   dbSNP   A 136 E - > G Bend 53% (Exposed) 1 158151954
    rs149463702 LS-SNP   dbSNP   A 179 S - > L Helix 77% (Exposed) 1 158152083
    rs147417067 LS-SNP   dbSNP   A 200 G - > D Bend 112% (Exposed) 1 158152713
    rs199860570 LS-SNP   dbSNP   A 201 R - > H Bend 37% (Exposed) 1 158152716
    rs139209490 LS-SNP   dbSNP   A 222 R - > W Coil 1% (Buried) 1 158152778
    rs149772303 LS-SNP   dbSNP   A 224 E - > D Bend 71% (Exposed) 1 158152786
    rs182855664 LS-SNP   dbSNP   A 241 E - > K Bend 36% (Exposed) 1 158152835
    rs200278882 LS-SNP   dbSNP   A 262 R - > Q Beta Ladder 19% (Intermediate) 1 158152899
    rs143328267 LS-SNP   dbSNP   A 266 S - > G Turn 39% (Exposed) 1 158152910
    rs140583445 LS-SNP   dbSNP   A 273 I - > F Beta Ladder 18% (Intermediate) 1 158152931
    rs145809444 LS-SNP   dbSNP   A 275 L - > P Beta Ladder 31% (Intermediate) 1 158152938
    rs142766597 LS-SNP   dbSNP   A 276 Y - > C Beta Ladder 72% (Exposed) 1 158152941
    rs11553032 LS-SNP   dbSNP   B 12 R - > C Bend 13% (Intermediate) 15 45007647
    rs11553035 LS-SNP   dbSNP   B 14 P - > S Coil 32% (Intermediate) 15 45007653
    rs11553038 LS-SNP   dbSNP   B 22 F - > L Beta Ladder 46% (Exposed) 15 45007677
    rs148494241 LS-SNP   dbSNP   B 34 D - > N Coil 31% (Intermediate) 15 45007713
    rs11553042 LS-SNP   dbSNP   B 36 E - > K Beta Ladder 41% (Exposed) 15 45007719
    rs11553049 LS-SNP   dbSNP   B 41 K - > R Beta Ladder 46% (Exposed) 15 45007735
    rs11553037 LS-SNP   dbSNP   B 53 D - > N Coil 27% (Intermediate) 15 45007770
    rs11553045 LS-SNP   dbSNP   B 72 P - > H Coil 1% (Buried) 15 45007828
    rs147708131 LS-SNP   dbSNP   B 99 M - > L Coil 18% (Intermediate) 15 45008535