8WUL

Crystal structure of affinity enhanced TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide (VVGAVGVGK)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and affinity enhancement of T-cell receptor targeting a KRAS G12V cancer neoantigen.

Zhang, M.Xu, W.Luo, L.Guan, F.Wang, X.Zhu, P.Zhang, J.Zhou, X.Wang, F.Ye, S.

(2024) Commun Biol 7: 512-512

  • DOI: https://doi.org/10.1038/s42003-024-06209-2
  • Primary Citation of Related Structures:  
    8WTE, 8WUL

  • PubMed Abstract: 

    Neoantigens derived from somatic mutations in Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS), the most frequently mutated oncogene, represent promising targets for cancer immunotherapy. Recent research highlights the potential role of human leukocyte antigen (HLA) allele A*11:01 in presenting these altered KRAS variants to the immune system. In this study, we successfully generate and identify murine T-cell receptors (TCRs) that specifically recognize KRAS 8-16 G12V from three predicted high affinity peptides. By determining the structure of the tumor-specific 4TCR2 bound to KRAS G12V -HLA-A*11:01, we conduct structure-based design to create and evaluate TCR variants with markedly enhanced affinity, up to 15.8-fold. This high-affinity TCR mutant, which involved only two amino acid substitutions, display minimal conformational alterations while maintaining a high degree of specificity for the KRAS G12V peptide. Our research unveils the molecular mechanisms governing TCR recognition towards KRAS G12V neoantigen and yields a range of affinity-enhanced TCR mutants with significant potential for immunotherapy strategies targeting tumors harboring the KRAS G12V mutation.


  • Organizational Affiliation

    Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TCR alpha chainA [auth C],
C [auth A],
E,
G
198Mus musculusMutation(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
TCR beta chainB [auth D],
D [auth B],
F,
H
239Mus musculusMutation(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 antigenI [auth L],
L [auth I],
O,
R
274Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A6M6CC39 (Homo sapiens)
Explore A0A6M6CC39 
Go to UniProtKB:  A0A6M6CC39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M6CC39
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinJ [auth M],
M [auth J],
P,
S
99Homo sapiensMutation(s): 0 
Gene Names: B2M
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
KRAS-G12V nonamer peptideK [auth N],
N [auth K],
Q,
T
9Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.752α = 94.556
b = 96.331β = 90.63
c = 123.121γ = 93.2
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFC2300503
Ministry of Science and Technology (MoST, China)China2021YFC2502300
Ministry of Science and Technology (MoST, China)China2022YFC2304705
Ministry of Science and Technology (MoST, China)China2022YFA0912400
Ministry of Science and Technology (MoST, China)China2020YFA0908500
National Natural Science Foundation of China (NSFC)China31971127

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references