7R7W | pdb_00007r7w

Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9 S3T variant

• PDB DOI: https://doi.org/10.2210/pdb7R7W/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, HIV-1 06TG.HT008
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-25 Released: 2022-06-29 
• Deposition Author(s): Li, X.L., Tan, K.M., Walker, B.D., Wang, J.H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

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

• PubMed: 37217466 
• DOI: https://doi.org/10.1038/s41467-023-38573-8
• Primary Citation 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.

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Organizational Affiliation: 
• School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China. [e-mail].
Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA. [e-mail].
Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA. [e-mail].
Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.
Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02142, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA.
IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA.
Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, 02114, USA.
Department of Chemistry, Columbia University, New York, NY, 10025, USA.
Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA. [e-mail].
Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA. [e-mail].
Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. [e-mail].
Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA. [e-mail].
Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA. [e-mail].
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02215, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.24 kDa 
• Atom Count: 3,895 
• Modeled Residue Count: 385 
• Deposited Residue Count: 387 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	278	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for S6BVK3 (Homo sapiens) Explore S6BVK3  Go to UniProtKB:  S6BVK3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP	C	9	HIV-1 06TG.HT008	Mutation(s): 0
UniProt
Find proteins for O91080 (Human immunodeficiency virus type 1 group N (isolate YBF30)) Explore O91080  Go to UniProtKB:  O91080

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.659	α = 90
b = 82.421	β = 90
c = 110.395	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Li, X.L., Tan, K.M., Walker, B.D., Wang, J.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 HL103526; R01 AI149704; 5UM1Al144462; P30 AI060354

Revision History  

• 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: 2024-11-13
  Changes: Structure summary