8GVG

The complex between public TCR TD08 and HLA-A24 bound to HIV-1 Nef138-8 (2F) peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.300 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors.

Ma, K.Chai, Y.Guan, J.Tan, S.Qi, J.Kawana-Tachikawa, A.Dong, T.Iwamoto, A.Shi, Y.Gao, G.F.

(2022) J Immunol 209: 1652-1661

  • DOI: https://doi.org/10.4049/jimmunol.2200191
  • Primary Citation of Related Structures:  
    8GVB, 8GVG, 8GVI

  • PubMed Abstract: 

    Cross-recognized public TCRs against HIV epitopes have been proposed to be important for the control of AIDS disease progression and HIV variants. The overlapping Nef138-8 and Nef138-10 peptides from the HIV Nef protein are HLA-A24-restricted immunodominant T cell epitopes, and an HIV mutant strain with a Y139F substitution in Nef protein can result in immune escape and is widespread in Japan. Here, we identified a pair of public TCRs specific to the HLA-A24-restricted Nef-138-8 epitope using PBMCs from White and Japanese patients, respectively, namely TD08 and H25-11. The gene use of the variable domain for TD08 and H25-11 is TRAV8-3, TRAJ10 for the α-chain and TRBV7-9, TRBD1*01, TRBJ2-5 for the β-chain. Both TCRs can recognize wild-type and Y2F-mutated Nef138-8 epitopes. We further determined three complex structures, including TD08/HLA-A24-Nef138-8, H25-11/HLA-A24-Nef138-8, and TD08/HLA-A24-Nef138-8 (2F). Then, we revealed the molecular basis of the public TCR binding to the peptide HLA, which mostly relies on the interaction between the TCR and HLA and can tolerate the mutation in the Nef138-8 peptide. These findings promote the molecular understanding of T cell immunity against HIV epitopes and provide an important basis for the engineering of TCRs to develop T cell-based immunotherapy against HIV infection.


  • Organizational Affiliation

    Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TD08 TCR alpha chain209Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TD08 TCR beta chain246Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigenC [auth H]275Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for F6IQZ4 (Homo sapiens)
Explore F6IQZ4 
Go to UniProtKB:  F6IQZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6IQZ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinD [auth L]100Homo 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
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
mutated 8-mer peptide from Protein NefE [auth P]8HIV whole-genome vector AA1305#18Mutation(s): 0 
UniProt
Find proteins for P04601 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04601 
Go to UniProtKB:  P04601
Entity Groups  
UniProt GroupP04601
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.300 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.035α = 90
b = 71.035β = 90
c = 383.869γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina2021YFC2300700

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary