7PDX

Crystal structure of parent MAGE-A10 TCR (728)

• PDB DOI: https://doi.org/10.2210/pdb7PDX/pdb

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


• Deposited: 2021-08-09 Released: 2022-08-03 
• Deposition Author(s): Simister, P.C., Border, E.C., Vieira, J.F., Pumphrey, N.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.252 
• R-Value Work: 0.192 

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

• PubMed: 35851311 
• 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.

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Organizational Affiliation: 

Adaptimmune, Abingdon, Oxfordshire, UK [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology, gel filtration

Macromolecule Content

• Total Structure Weight: 100.17 kDa 
• Atom Count: 7,061 
• Modelled Residue Count: 875 
• Deposited Residue Count: 894 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor alpha chain (TRAV/TRAC)	A [auth CCC], C [auth AAA]	206	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell receptor beta chain (TRBV/TRBC)	B [auth DDD], D [auth BBB]	241	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth BBB]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	E [auth DDD], G [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.252 
• R-Value Work: 0.192 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.93	α = 101.94
b = 59.171	β = 105.87
c = 86.02	γ = 104.69

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOSFLM	data reduction
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Simister, P.C., Border, E.C., Vieira, J.F., Pumphrey, N.J.

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Funding Organization	Location	Grant Number
Other private	United Kingdom	--

Revision History  

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