9IKY | pdb_00009iky

Crystal structure of 1-2C-T96F TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide (VVGAVGVGK)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 
    0.234 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An Engineered Soluble Single-Chain TCR Engager for KRAS-G12V Specific Tumor Immunotherapy.

Ma, K.Wang, J.Jiang, M.He, J.Li, F.Lu, D.Su, C.Chai, Y.Jin, W.Chen, Y.Zhang, C.W.H.Ma, X.Tan, H.Gao, G.F.Tan, S.

(2025) Adv Sci (Weinh) 12: e00181-e00181

  • DOI: https://doi.org/10.1002/advs.202500181
  • Primary Citation of Related Structures:  
    9IKY

  • PubMed Abstract: 

    T cell receptor (TCR) based immunotherapy is an attractive strategy to target a wide range of intra-tumoral antigens and elicit robust tumor cytotoxicity. However, engineering soluble TCR engagers that preserve physiological affinity is crucial for universal TCR drug development, yet remains challenging. In the present study, multiple TCR engagers featuring diverse architectures based on the KRAS-G12V specific 1-2C TCR in the context of HLA-A*11:01 is designed and evaluated. Notably, a soluble tandem double single-chain TCR (STanD-scTCR) engager, comprising two repeated single-chain variable fragment (scFv) TCRs, exhibit enhanced binding avidity and potent T-cell activation. Through site-directed mutagenesis, T96F mutation (T96F-TCR) within the TCR β chain is identified, which substantially augment T cell reactivity while maintaining physiological affinity and minimizing off-target cross-reactivity. The T96F-mutated STanD-scTCR engager demonstrates improved antigen sensitivity, promotes multi-functional T-cell responses, and facilitates immune synapse formation between T cells and target cells. In a xenograft tumor model harboring the KRAS-G12V mutation, the TCR engager displays substantial tumor suppression efficacy. These findings underscore the therapeutic potential of 1-2C STanD-scTCR engage in targeting KRAS-G12V mutations in the context of HLA-A*11:01. Furthermore, the engineering strategies employ in the development of STanD-scTCR engager provide an invaluable for future designs of TCR engager drugs.


  • Organizational Affiliation
    • Department of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, 518026, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen275Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A6M6CC39 (Homo sapiens)
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Go to UniProtKB:  A0A6M6CC39
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UniProt GroupA0A6M6CC39
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo 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 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VAL-VAL-GLY-ALA-VAL-GLY-VAL-GLY-LYS9Kirsten murine sarcoma virusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
1-2C-T96F TCR alpha chain204Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
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UniProt GroupP01848
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
1-2C-T96F TCR beta chain242Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free:  0.234 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.775α = 103.03
b = 157.773β = 101.92
c = 193.023γ = 82.17
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China92169208
National Natural Science Foundation of China (NSFC)China32222031

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Database references