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RCSB PDB - 4U1L: HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes

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HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes



    This is version 2.2 of the entry. See complete history. 



    A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape.

    Klverpris, H.N., Cole, D.K., Fuller, A., Carlson, J., Beck, K., Schauenburg, A.J., Rizkallah, P.J., Buus, S., Sewell, A.K., Goulder, P.

    (2015) Retrovirology 12: 20-20

    • PubMed: 25808313 Search on PubMedSearch on PubMed Central
    • DOI: https://doi.org/10.1186/s12977-015-0149-5

    • PubMed Abstract: 

      Presentation of identical HIV-1 peptides by closely related Human Leukocyte Antigen class I (HLAI) molecules can select distinct patterns of escape mutation that have a significant impact on viral fitness and disease progression. The molecular mechanisms by which HLAI micropolymorphisms can induce differential HIV-1 escape patterns within identical peptide epitopes remain unknown. Here, we undertook genetic and structural analyses of two immunodominant HIV-1 peptides, Gag180-188 (TPQDLNTML, TL9-p24) and Nef71-79 (RPQVPLRPM, RM9-Nef) that are among the most highly targeted epitopes in the global HIV-1 epidemic. We show that single polymorphisms between different alleles of the HLA-B7 superfamily can induce a conformational switch in peptide conformation that is associated with differential HLAI-specific escape mutation and immune control. A dominant R71K mutation in the Nef71-79 occurred in those with HLA-B*07:02 but not B*42:01/02 or B*81:01. No structural difference in the HLA-epitope complexes was detected to explain this observation. These data suggest that identical peptides presented through very similar HLAI landscapes are recognized as distinct epitopes and provide a novel structural mechanism for previously observed differential HIV-1 escape and disease progression.

    Macromolecule Content

    • Total Structure Weight: 91.65 kDa 
    • Atom Count: 6,806 
    • Modelled Residue Count: 772 
    • Deposited Residue Count: 772 
    • Unique protein chains: 3

    Find similar proteins by:

    (by identity cutoff)  |  3D Structure

    Find similar proteins by:

    (by identity cutoff)  |  3D Structure

    Find similar proteins by:  Sequence   |   3D Structure  

    Entity ID: 3
    MoleculeChains Sequence LengthOrganismDetailsImage
    Protein Nef

    C, F

    		9Human immunodeficiency virus 1Mutation(s): 0 
    UniProt

    Find proteins for P03407 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))

    Explore P03407 

    Go to UniProtKB:  P03407

    Entity Groups  
    UniProt GroupP03407
    Sequence Annotations
    Expand
    • Reference Sequence
    Ligands 3 Unique
    IDChains Name / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4
    Download Ideal Coordinates CCD File 
    		N [auth A],
    O [auth A]    		SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
    GOL
    Query on GOL
    Download Ideal Coordinates CCD File 
    		G [auth A],
    H [auth A],
    Q [auth D]    		GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
    EDO
    Query on EDO
    Download Ideal Coordinates CCD File 

    AA [auth E]
    BA [auth E]
    CA [auth F]
    I [auth A]
    J [auth A]

    AA [auth E],
    BA [auth E],
    CA [auth F],
    I [auth A],
    J [auth A],
    K [auth A],
    L [auth A],
    M [auth A],
    P [auth B],
    R [auth D],
    S [auth D],
    T [auth D],
    U [auth D],
    V [auth D],
    W [auth D],
    X [auth D],
    Y [auth D],
    Z [auth D]

    		1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N

    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.06 Å
    • R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
    • R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
    • R-Value Observed: 0.175 (Depositor) 

    Unit Cell:

    Length ( Å )Angle ( ˚ )
    a = 46.02α = 91.13
    b = 49.06β = 93.53
    c = 107.84γ = 95.7

    Software Package:

    Software NamePurpose
    XDSdata reduction
    Aimlessdata scaling
    PDB_EXTRACTdata extraction
    PHASERphasing
    REFMACrefinement
    GDAdata reduction

    Entry History & Funding Information

    Deposition Data

    Funding OrganizationLocationGrant Number
    Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/H001085/1

    Revision History  (Full details and data files)

    • Version 1.0: 2015-04-08
      Type: Initial release
    • Version 2.0: 2017-08-30
      Changes: Atomic model, Author supporting evidence, Derived calculations
    • Version 2.1: 2023-12-20
      Changes: Data collection, Database references, Refinement description
    • Version 2.2: 2024-11-06
      Changes: Structure summary