8RO5 | pdb_00008ro5

HLA-A3 restricted mG12V-TCR

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-01-11 Released: 2025-01-22 
  • Deposition Author(s): Sim, M.J.W., Sun, P.D.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.209 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RO5

This is version 1.0 of the entry. See complete history

Literature

Identification and structural characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3.

Sim, M.J.W.Hanada, K.I.Stotz, Z.Yu, Z.Lu, J.Brennan, P.Quastel, M.Gillespie, G.M.Long, E.O.Yang, J.C.Sun, P.D.

(2024) Eur J Immunol 54: e2451079-e2451079

  • DOI: https://doi.org/10.1002/eji.202451079
  • Primary Citation Related Structures: 
    8RNI, 8RO5, 8RRO, 8VJZ

  • PubMed Abstract: 

    Mutations in KRAS are some of the most common across multiple cancer types and are thus attractive targets for therapy. Recent studies demonstrated that mutant KRAS generates immunogenic neoantigens that are targetable by adoptive T-cell therapy in metastatic diseases. To expand mutant KRAS-specific immunotherapies, it is critical to identify additional HLA-I allotypes that can present KRAS neoantigens and their cognate T-cell receptors (TCR). Here, we identified a murine TCR specific to a KRAS-G12V neoantigen ( 7 VVVGAVGVGK 16 ) using a vaccination approach with transgenic mice expressing HLA-A*03:01 (HLA-A3). This TCR demonstrated exquisite specificity for mutant G12V and not WT KRAS peptides. To investigate the molecular basis for neoantigen recognition by this TCR, we determined its structure in complex with HLA-A3(G12V). G12V-TCR CDR3β and CDR1β formed a hydrophobic pocket to interact with p6 Val of the G12V but not the WT KRAS peptide. To improve the tumor sensitivity of this TCR, we designed rational substitutions to improve TCR:HLA-A3 contacts. Two substitutions exhibited modest improvements in TCR binding avidity to HLA-A3 (G12V) but did not sufficiently improve T-cell sensitivity for further clinical development. Our study provides mechanistic insight into how TCRs detect neoantigens and reveals the challenges in targeting KRAS-G12V mutations.


  • Organizational Affiliation
    • Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA.

Macromolecule Content 

  • Total Structure Weight: 50.45 kDa 
  • Atom Count: 3,904 
  • Modeled Residue Count: 444 
  • Deposited Residue Count: 444 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chains: BA [auth B]241Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chains: AB [auth A]203Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.209 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.575α = 90
b = 43.32β = 108.5
c = 84.243γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release