8ESB | pdb_00008esb

CryoEM structure of HLA-A2 bound to MAGEA8 (232-241) peptide

• PDB DOI: https://doi.org/10.2210/pdb8ESB/pdb
• EM Map EMD-28574: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-10-13 Released: 2023-05-03 
• Deposition Author(s): Saotome, K., Franklin, M.C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM.

Saotome, K., Dudgeon, D., Colotti, K., Moore, M.J., Jones, J., Zhou, Y., Rafique, A., Yancopoulos, G.D., Murphy, A.J., Lin, J.C., Olson, W.C., Franklin, M.C.

(2023) Nat Commun 14: 2401-2401

• PubMed: 37100770 
• DOI: https://doi.org/10.1038/s41467-023-37532-7
• Primary Citation Related Structures: 
  8ES7, 8ES8, 8ES9, 8ESA, 8ESB


• PubMed Abstract: 
  

  The recognition of antigenic peptide-MHC (pMHC) molecules by T-cell receptors (TCR) initiates the T-cell mediated immune response. Structural characterization is key for understanding the specificity of TCR-pMHC interactions and informing the development of therapeutics. Despite the rapid rise of single particle cryoelectron microscopy (cryoEM), x-ray crystallography has remained the preferred method for structure determination of TCR-pMHC complexes. Here, we report cryoEM structures of two distinct full-length α/β TCR-CD3 complexes bound to their pMHC ligand, the cancer-testis antigen HLA-A2/MAGEA4 (230-239). We also determined cryoEM structures of pMHCs containing MAGEA4 (230-239) peptide and the closely related MAGEA8 (232-241) peptide in the absence of TCR, which provided a structural explanation for the MAGEA4 preference displayed by the TCRs. These findings provide insights into the TCR recognition of a clinically relevant cancer antigen and demonstrate the utility of cryoEM for high-resolution structural analysis of TCR-pMHC interactions.

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Organizational Affiliation: 
• Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA. [e-mail].
Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 150.92 kDa 
• Atom Count: 3,140 
• Modeled Residue Count: 384 
• Deposited Residue Count: 1,344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin,HLA class I antigen,MAGE-A8 peptide chimera	A, B, C	448	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q53Z42 (Homo sapiens) Explore Q53Z42  Go to UniProtKB:  Q53Z42

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): Saotome, K., Franklin, M.C.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Structure summary