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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 A,C
    GO ID   Ontology GO Term Definition
    6955   Immune Response  Any Immune System Process That Functions in the Calibrated Response of an Organism to a Potential Internal or Invasive Threat. 
    19882   Antigen Processing and Presentation  The Process in Which an Antigen Presenting Cell Expresses Antigen (peptide or Lipid) On Its Cell Surface in Association with an Mhc Protein Complex. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    Chain B,D
    GO ID   Ontology GO Term Definition
    1895   Retina Homeostasis  A Tissue Homeostatic Process Involved in the Maintenance of an Internal Equilibrium Within the Retina of the Eye Including Control of Cellular Proliferation and Death and Control of Metabolic Function. 
    1916   Positive Regulation of T Cell Mediated Cytotoxicity  Any Process That Activates or Increases the Frequency Rate or Extent of T Cell Mediated Cytotoxicity. 
    2237   Response to Molecule of Bacterial Origin  Any Process That Results in a Change in State or Activity of an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus by Molecules of Bacterial Origin Such As Peptides Derived From Bacterial Flagellin. 
    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. 
    2479   Antigen Processing and Presentation of Exogenous Peptide Antigen Via Mhc Class I Tap Dependent  The Process in Which an Antigen Presenting Cell Expresses a Peptide Antigen of Exogenous Origin On Its Cell Surface in Association with an Mhc Class I Protein Complex Following Intracellular Transport Via a Tap (transporter Associated with Antigen Processing) Pathway. the Peptide Is Typically a Fragment of a Larger Exogenous Protein Which Has Been Degraded Within the Cell and Is Dependent On Tap Transport From the Cytosol to Er For Association with the Mhc Class I Molecule. Class I Here Refers to Classical Class I Molecules. 
    2480   Antigen Processing and Presentation of Exogenous Peptide Antigen Via Mhc Class I Tap Independent  The Process in Which an Antigen Presenting Cell Expresses a Peptide Antigen of Exogenous Origin On Its Cell Surface in Association with an Mhc Class I Protein Complex Following Intracellular Transport Via a Pathway Not Requiring Tap (transporter Associated with Antigen Processing). the Peptide Is Typically a Fragment of a Larger Exogenous Protein Which Has Been Degraded Within the Cell. Class I Here Refers to Classical Class I Molecules. 
    2481   Antigen Processing and Presentation of Exogenous Protein Antigen Via Mhc Class Ib Tap Dependent  The Process in Which an Antigen Presenting Cell Expresses a Peptide Antigen of Exogenous Origin On Its Cell Surface in Association with an Mhc Class Ib Protein Complex Following Intracellular Transport Via a Tap (transporter Associated with Antigen Processing) Pathway. the Peptide Is Typically a Fragment of a Larger Exogenous Protein Which Has Been Degraded Within the Cell and Is Dependent On Tap Transport From the Cytosol to Er For Association with the Mhc Class Ib Molecule. Class Ib Here Refers to Non Classical Class I Molecules Such As Those of the Hla E Gene Family. 
    16032   Viral Process  A Multi Organism Process in Which a Virus Is a Participant. the Other Participant Is the Host. Includes Infection of a Host Cell Replication of the Viral Genome and Assembly of Progeny Virus Particles. in Some Cases the Viral Genetic Material May Integrate Into the Host Genome and Only Subsequently Under Particular Circumstances 'complete' Its Life Cycle. 
    19221   Cytokine Mediated Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of a Cytokine to a Receptor On the Surface of a Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    33077   T Cell Differentiation in Thymus  The Process in Which a Precursor Cell Type Acquires the Specialized Features of a T Cell Via a Differentiation Pathway Dependent Upon Transit Through the Thymus. 
    42026   Protein Refolding  The Process Carried Out by a Cell That Restores the Biological Activity of an Unfolded or Misfolded Protein Using Helper Proteins Such As Chaperones. 
    42493   Response to Drug  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Drug Stimulus. a Drug Is a Substance Used in the Diagnosis Treatment or Prevention of a Disease. 
    42590   Antigen Processing and Presentation of Exogenous Peptide Antigen Via Mhc Class I  The Process in Which an Antigen Presenting Cell Expresses a Peptide Antigen of Exogenous Origin On Its Cell Surface in Association with an Mhc Class I Protein Complex. the Peptide Antigen Is Typically But Not Always Processed From a Whole Protein. Class I Here Refers to Classical Class I Molecules. 
    45087   Innate Immune Response  Innate Immune Responses Are Defense Responses Mediated by Germline Encoded Components That Directly Recognize Components of Potential Pathogens. 
    46686   Response to Cadmium Ion  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Cadmium (cd) Ion Stimulus. 
    50690   Regulation of Defense Response to Virus by Virus  Any Viral Process That Modulates the Frequency Rate or Extent of the Antiviral Response of the Host Cell or Organism. 
    50776   Regulation of Immune Response  Any Process That Modulates the Frequency Rate or Extent of the Immune Response the Immunological Reaction of an Organism to an Immunogenic Stimulus. 
    60333   Interferon Gamma Mediated Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of Interferon Gamma to a Receptor On the Surface of a Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. Interferon Gamma Is the Only Member of the Type Ii Interferon Found So Far. 
    139   Golgi Membrane  The Lipid Bilayer Surrounding Any of the Compartments of the Golgi Apparatus. 
    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. 
    5615   Extracellular Space  That Part of a Multicellular Organism Outside the Cells Proper Usually Taken to Be Outside the Plasma Membranes and Occupied by Fluid. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5788   Endoplasmic Reticulum Lumen  The Volume Enclosed by the Membranes of the Endoplasmic Reticulum. 
    5794   Golgi Apparatus  A Compound Membranous Cytoplasmic Organelle of Eukaryotic Cells Consisting of Flattened Ribosome Free Vesicles Arranged in a More or Less Regular Stack. the Golgi Apparatus Differs From the Endoplasmic Reticulum in Often Having Slightly Thicker Membranes Appearing in Sections As a Characteristic Shallow Semicircle So That the Convex Side (cis or Entry Face) Abuts the Endoplasmic Reticulum Secretory Vesicles Emerging From the Concave Side (trans or Exit Face). in Vertebrate Cells There Is Usually One Such Organelle While in Invertebrates and Plants Where They Are Known Usually As Dictyosomes There May Be Several Scattered in the Cytoplasm. the Golgi Apparatus Processes Proteins Produced On the Ribosomes of the Rough Endoplasmic Reticulum; Such Processing Includes Modification of the Core Oligosaccharides of Glycoproteins and the Sorting and Packaging of Proteins For Transport to a Variety of Cellular Locations. Three Different Regions of the Golgi Are Now Recognized Both in Terms of Structure and Function: Cis in the Vicinity of the Cis Face Trans in the Vicinity of the Trans Face and Medial Lying Between the Cis and Trans Regions. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    5925   Focal Adhesion  Small Region On the Surface of a Cell That Anchors the Cell to the Extracellular Matrix and That Forms a Point of Termination of Actin Filaments. 
    9897   External Side of Plasma Membrane  The Leaflet the Plasma Membrane That Faces Away From the Cytoplasm and Any Proteins Embedded or Anchored in It or Attached to Its Surface. 
    12507   Er to Golgi Transport Vesicle Membrane  The Lipid Bilayer Surrounding a Vesicle Transporting Substances From the Endoplasmic Reticulum to the Golgi. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    30670   Phagocytic Vesicle Membrane  The Lipid Bilayer Surrounding a Phagocytic Vesicle. 
    31901   Early Endosome Membrane  The Lipid Bilayer Surrounding an Early Endosome. 
    31905   Early Endosome Lumen  The Volume Enclosed by the Membrane of an Early Endosome. 
    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. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    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