7PDW

Crystal structure of parent TCR (728) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into engineering a T-cell receptor targeting MAGE-A10 with higher affinity and specificity for cancer immunotherapy.

Simister, P.C.Border, E.C.Vieira, J.F.Pumphrey, N.J.

(2022) J Immunother Cancer 10

  • DOI: https://doi.org/10.1136/jitc-2022-004600
  • Primary Citation of Related Structures:  
    7PBC, 7PDW, 7PDX, 7QPJ

  • PubMed Abstract: 

    T-cell receptor (TCR) immunotherapy is becoming a viable modality in cancer treatment with efficacy in clinical trials. The safety of patients is paramount, so innovative cell engineering methods are being employed to exploit adaptive immunity while controlling the factors governing antigen receptor (ie, TCR) specificity and cross-reactivity. We recently reported a TCR engineering campaign and selectivity profiling assay (X-scan) targeting a melanoma antigen gene (MAGE)-A10 peptide. This helped to distinguish between two well-performing TCRs based on cross-reactivity potential during preclinical drug evaluation, allowing one to be advanced to T-cell immunotherapeutic clinical trials. Here, we present three-dimensional structural information on those TCRs, highlighting engineering improvements and molecular mechanisms likely underpinning differential selectivity.


  • Organizational Affiliation

    Adaptimmune, Abingdon, Oxfordshire, UK Philip.Simister@adaptimmune.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor alpha chain (TRAV/TRAC)A [auth AAA],
E [auth FFF]
206Homo 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
T-cell receptor beta chain (TRBV/TRBC)B [auth BBB],
F [auth GGG]
241Homo 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
Beta-2-microglobulinC [auth DDD],
G [auth III]
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Melanoma-associated antigen 10D [auth EEE],
H [auth JJJ]
9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P43363 (Homo sapiens)
Explore P43363 
Go to UniProtKB:  P43363
PHAROS:  P43363
GTEx:  ENSG00000124260 
Entity Groups  
UniProt GroupP43363
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigenI [auth CCC],
J [auth HHH]
277Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for Q861F7 (Homo sapiens)
Explore Q861F7 
Go to UniProtKB:  Q861F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ861F7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.081α = 109.17
b = 95.834β = 96.51
c = 106.261γ = 99.7
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description