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Newly identified epitope N1 derived from SARS-CoV N protein complexed with HLA-A*2402
Biology and Chemistry Report
3I6L
  •   Structure Details   Hide

    Structure Keywords

    Keywords Immune System
    Text HLA-A*2402, SARS-CoV, nucleocapsid protein, Disulfide bond, Glycoprotein, Host-virus interaction, Immune response, Membrane, MHC I, Transmembrane, Disease mutation, Glycation, Immunoglobulin domain, Pyrrolidone carboxylic acid, Secreted, Golgi apparatus, Phosphoprotein, Ribonucleoprotein, RNA-binding, Viral nucleoprotein, Virion, Immune System

    Polymeric Molecules

    Chain D
    Description HLA class I histocompatibility antigen, A-24 alpha chain 
    Fragment alpha 1-3 regions, UNP residues 25-298 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 31552.1 
    Source Method genetically manipulated  
    Entity Name MHC class I antigen HLA-A*2402, MHC class I antigen A*24, Aw-24, A-9 
    Chain E
    Description Beta-2-microglobulin 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11879.5 
    Source Method genetically manipulated  
    Entity Name Beta-2-microglobulin form pI 5.3 
    Chain F
    Description Nucleoprotein peptide 
    Fragment UNP residue 346-354 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 1090.3 
    Source Method synthetic  
    Entity Name peptide N1, Nucleocapsid protein, Protein N, NC 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    D 1A24_HUMAN P05534     
    E B2MG_HUMAN P61769     
    F NCAP_CVHSA P59595     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 50779    
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain E
    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 E
    Common Name Human
    Scientific Name Homo sapiens  
    Gene b2m, beta-2-microglobulin, cdabp0092, hdcma22p
    Host Scientific Name Escherichia coli  
    Host Strain Bl21 (de3)
    Host Vector Type Plasmid
    Host Plasmid Name pGMT7


    Chain D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene hla-a, hlaa, mhc class i antigen hla-a*2402
    Host Scientific Name Escherichia coli  
    Host Strain Bl21 (de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET28a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6p21.3 3105     major histocompatibility complex, class I, A HLA-A    
    15 15q21-q22.2 567     beta-2-microglobulin B2M    
    - - 1489678     nucleocapsid protein N    

    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
    rs11553032 LS-SNP   dbSNP   E 12 R - > C Bend 18% (Intermediate) 15 45007647
    rs11553035 LS-SNP   dbSNP   E 14 P - > S Coil 73% (Exposed) 15 45007653
    rs11553038 LS-SNP   dbSNP   E 22 F - > L Beta Ladder 23% (Intermediate) 15 45007677
    rs148494241 LS-SNP   dbSNP   E 34 D - > N Coil 54% (Exposed) 15 45007713
    rs11553042 LS-SNP   dbSNP   E 36 E - > K Beta Ladder 55% (Exposed) 15 45007719
    rs11553049 LS-SNP   dbSNP   E 41 K - > R Beta Ladder 47% (Exposed) 15 45007735
    rs11553037 LS-SNP   dbSNP   E 53 D - > N Coil 8% (Buried) 15 45007770
    rs11553045 LS-SNP   dbSNP   E 72 P - > H Coil 0% (Buried) 15 45007828
    rs147708131 LS-SNP   dbSNP   E 99 M - > L Coil 28% (Intermediate) 15 45008535