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Crystal structure of HLA-DM bound to HLA-DR1
Biology and Chemistry Report
4FQX
  •   Structure Details   Hide

    Structure Keywords

    Keywords IMMUNE SYSTEM
    Text immune complex, peptide loading, peptide editing, antigen presentation, IMMUNE SYSTEM

    Polymeric Molecules

    Chain C
    Description HLA class II histocompatibility antigen, DM alpha chain 
    Fragment unp residues 27-225 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 22993.1 
    Source Method genetically manipulated  
    Entity Name MHC class II antigen DMA, Really interesting new gene 6 protein 
    Chain D
    Description HLA class II histocompatibility antigen, DM beta chain 
    Fragment unp residues 19-211 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 22233.3 
    Source Method genetically manipulated  
    Entity Name MHC class II antigen DMB, Really interesting new gene 7 protein 
    Chain E
    Description Synthetic peptide 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 1206.5 
    Source Method synthetic  
    Chain A
    Description HLA class II histocompatibility antigen, DR alpha chain 
    Fragment unp residues 26-216 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 22112.1 
    Source Method genetically manipulated  
    Entity Name MHC class II antigen DRA 
    Chain B
    Description HLA class II histocompatibility antigen, DRB1-1 beta chain 
    Fragment unp residues 30-221 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23735.6 
    Source Method genetically manipulated  
    Entity Name MHC class II antigen DRB1*1, DR-1, DR1 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A DRA_HUMAN A2BET4     
    B 2B11_HUMAN A4F5N0     
    C DMA_HUMAN P28067     
    D DMB_HUMAN O77936     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 179797    
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    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. 
    42613   Mhc Class Ii Protein Complex  A Transmembrane Protein Complex Composed of an Mhc Class Ii Alpha and Mhc Class Ii Beta Chain and with or Without a Bound Peptide or Polysaccharide Antigen. 
    Chain B
    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. 
    42613   Mhc Class Ii Protein Complex  A Transmembrane Protein Complex Composed of an Mhc Class Ii Alpha and Mhc Class Ii Beta Chain and with or Without a Bound Peptide or Polysaccharide Antigen. 
    Chain 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. 
    42613   Mhc Class Ii Protein Complex  A Transmembrane Protein Complex Composed of an Mhc Class Ii Alpha and Mhc Class Ii Beta Chain and with or Without a Bound Peptide or Polysaccharide Antigen. 
    Chain D
    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. 
    42613   Mhc Class Ii Protein Complex  A Transmembrane Protein Complex Composed of an Mhc Class Ii Alpha and Mhc Class Ii Beta Chain and with or Without a Bound Peptide or Polysaccharide Antigen. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene beta chain, hla-dr1, hla-drb1, mhc class ii molecule
    Host Scientific Name Spodoptera frugiperda  


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene hla-dr1 alpha chain, hla-dra, hla-dra1, mhc class ii molecule
    Host Scientific Name Spodoptera frugiperda  


    Chain D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene dm beta chain, dmb, hla class ii histocompatibility antigen, hla-dmb, ring7
    Host Scientific Name Cricetulus griseus  
    Host Strain Lec3.2.8.1
    Host Vector Type Plasmid
    Host Plasmid Name pEE14.1


    Chain C
    Common Name Human
    Scientific Name Homo sapiens  
    Gene dm alpha chain, dma, hla class ii histocompatibility antigen, hla-dma, ring6
    Host Scientific Name Spodoptera frugiperda  
    Host Strain Lec3.2.8.1
    Host Vector Type Plasmid
    Host Plasmid Name pEE14.1


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6p21.3 3108     major histocompatibility complex, class II, DM alpha HLA-DMA    
    6 6p21.3 3109     major histocompatibility complex, class II, DM beta HLA-DMB    
    6 6p21.3 3122     major histocompatibility complex, class II, DR alpha HLA-DRA    
    6 6p21.3 3123     major histocompatibility complex, class II, DR beta 1 HLA-DRB1    

    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
    rs201781094 LS-SNP   dbSNP   A 76 R - > S Helix 25% (Intermediate) 6_ssto_hap7 3757105
    rs144120198 LS-SNP   dbSNP   A 88 E - > K Beta Ladder 55% (Exposed) 6_ssto_hap7 3757632
    rs138462914 LS-SNP   dbSNP   A 123 R - > Q Beta Ladder 26% (Intermediate) 6_ssto_hap7 3757738
    rs146370028 LS-SNP   dbSNP   A 153 F - > L Beta Ladder 0% (Buried) 6 32411165
    rs200798853 LS-SNP   dbSNP   A 160 V - > I Beta Ladder 25% (Intermediate) 6_ssto_hap7 3757848
    rs199723815 LS-SNP   dbSNP   A 168 W - > R Turn 33% (Intermediate) 6_ssto_hap7 3757872 NAG