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Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody
Biology and Chemistry Report
2B4C
  •   Structure Details   Hide

    Structure Keywords

    Keywords Viral protein/Immune system
    Text HIV-1, gp120, JRFL, V3, X5, CD4 induced antibody, Viral protein-Immune system COMPLEX

    Polymeric Molecules

    Chain G
    Description envelope glycoprotein 
    Fragment CORE with V3 
    Mutation N301Q, T389A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 38453.0 
    Source Method genetically manipulated  
    Chain C
    Description T-cell surface glycoprotein CD4 
    Fragment D1D2, N-TERMINAL TWO DOMAIN FRAGMENT 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 20130.1 
    Source Method genetically manipulated  
    Entity Name T-cell surface antigen T4/Leu-3 
    Chain L
    Description anti-HIV-1 gp120 immunoglobulin X5 light chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23268.0 
    Source Method genetically manipulated  
    Chain H
    Description anti-HIV-1 gp120 immunoglobulin X5 heavy chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 24990.9 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    FUC  ALPHA-L-FUCOSE  C6 H12 O5   164.16  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    NDG  2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE  C8 H15 N O6   221.21  View 
    SO4  SULFATE ION  O4 S   96.06  View 
    XYL  D-XYLITOL  C5 H12 O5   152.15  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    C CD4_HUMAN B2R737     
    G Q75760_9HIV1 Q75760     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 164098    
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain C
    GO ID   Ontology GO Term Definition
    7155   Cell Adhesion  The Attachment of a Cell Either to Another Cell or to an Underlying Substrate Such As the Extracellular Matrix Via Cell Adhesion Molecules. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    Chain G
    GO ID   Ontology GO Term Definition
    19031   Viral Envelope  The Lipid Bilayer of a Virion That Surrounds the Protein Capsid. May Also Contain Glycoproteins. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain H
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Chain L
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia


    Chain C
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene cd4
    Host Common Name Chinese Hamster
    Host Scientific Name Cricetulus griseus  
    Host Genus Cricetulus


    Chain G
    Scientific Name Human immunodeficiency virus 1  
    Genus Lentivirus
    Host Common Name Fruit Fly
    Host Scientific Name Drosophila melanogaster  
    Host Genus Drosophila


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    12 12p13.31 920     CD4 molecule CD4    

    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
    rs199890832 LS-SNP   dbSNP   C 34 I - > K Coil 27% (Intermediate) 12 6909599
    rs201991979 LS-SNP   dbSNP   C 40 Q - > R Bend 5% (Buried) 12 6909617
    rs200264344 LS-SNP   dbSNP   C 54 R - > C Turn 11% (Intermediate) 12 6923328
    rs201343243 LS-SNP   dbSNP   C 55 A - > ST Beta Ladder 0% (Buried) 12 6923331
    rs200573785 LS-SNP   dbSNP   C 56 D - > V Beta Ladder 31% (Intermediate) 12 6923335
    rs141281945 LS-SNP   dbSNP   C 70 I - > T Beta Ladder 29% (Intermediate) 12 6923377
    rs201280254 LS-SNP   dbSNP   C 79 S - > T Coil 18% (Intermediate) 12 6923403
    rs202208698 LS-SNP   dbSNP   C 111 G - > R Turn 64% (Exposed) 12 6923957
    rs202028153 LS-SNP   dbSNP   C 122 P - > S Bend 101% (Exposed) 12 6923990
    rs201323005 LS-SNP   dbSNP   C 123 G - > D Bend 99% (Exposed) 12 6923994
    rs200491526 LS-SNP   dbSNP   C 138 I - > M Beta Ladder 14% (Intermediate) 12 6924040
    rs191620221 LS-SNP   dbSNP   C 139 Q - > E Beta Ladder 72% (Exposed) 12 6924041
    rs201435903 LS-SNP   dbSNP   C 140 G - > V Coil 61% (Exposed) 12 6924045
    rs201423104 LS-SNP   dbSNP   C 142 K - > T Bend 71% (Exposed) 12 6924051
    rs200162977 LS-SNP   dbSNP   C 146 V - > M Beta Ladder 15% (Intermediate) 12 6924062
    rs201315085 LS-SNP   dbSNP   C 161 V - > L Beta Ladder 1% (Buried) 12 6924107
    rs143646863 LS-SNP   dbSNP   C 165 Q - > R Turn 92% (Exposed) 12 6924120
    rs28917504 LS-SNP   dbSNP   C 166 K - > E Beta Ladder 49% (Exposed) 12 6924122
    rs199799041 LS-SNP   dbSNP   C 172 I - > T Beta Ladder 24% (Intermediate) 12 6924141
    rs140406047 LS-SNP   dbSNP   C 175 V - > LM Coil 65% (Exposed) 12 6924149