7R7Y

Crystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived epitope QW9 S3T variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide.

Li, X.Singh, N.K.Collins, D.R.Ng, R.Zhang, A.Lamothe-Molina, P.A.Shahinian, P.Xu, S.Tan, K.Piechocka-Trocha, A.Urbach, J.M.Weber, J.K.Gaiha, G.D.Takou Mbah, O.C.Huynh, T.Cheever, S.Chen, J.Birnbaum, M.Zhou, R.Walker, B.D.Wang, J.H.

(2023) Nat Commun 14: 2929-2929

  • DOI: https://doi.org/10.1038/s41467-023-38573-8
  • Primary Citation of Related Structures:  
    7R7V, 7R7W, 7R7X, 7R7Y, 7R7Z, 7R80

  • PubMed Abstract: 

    Cytotoxic-T-lymphocyte (CTL) mediated control of HIV-1 is enhanced by targeting highly networked epitopes in complex with human-leukocyte-antigen-class-I (HLA-I). However, the extent to which the presenting HLA allele contributes to this process is unknown. Here we examine the CTL response to QW9, a highly networked epitope presented by the disease-protective HLA-B57 and disease-neutral HLA-B53. Despite robust targeting of QW9 in persons expressing either allele, T cell receptor (TCR) cross-recognition of the naturally occurring variant QW9_S3T is consistently reduced when presented by HLA-B53 but not by HLA-B57. Crystal structures show substantial conformational changes from QW9-HLA to QW9_S3T-HLA by both alleles. The TCR-QW9-B53 ternary complex structure manifests how the QW9-B53 can elicit effective CTLs and suggests sterically hindered cross-recognition by QW9_S3T-B53. We observe populations of cross-reactive TCRs for B57, but not B53 and also find greater peptide-HLA stability for B57 in comparison to B53. These data demonstrate differential impacts of HLAs on TCR cross-recognition and antigen presentation of a naturally arising variant, with important implications for vaccine design.


  • Organizational Affiliation

    School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China. xiaolong@crystal.harvard.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen276Homo sapiensMutation(s): 0 
Gene Names: HLA-B
UniProt
Find proteins for U6BR87 (Homo sapiens)
Explore U6BR87 
Go to UniProtKB:  U6BR87
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU6BR87
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP9HIV-1 06TG.HT008Mutation(s): 0 
UniProt
Find proteins for O91080 (Human immunodeficiency virus type 1 group N (isolate YBF30))
Explore O91080 
Go to UniProtKB:  O91080
Entity Groups  
UniProt GroupO91080
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.335α = 90
b = 81.828β = 90
c = 109.92γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 HL103526; R01 AI149704; 5UM1Al144462; P30 AI060354

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary