9RXM | pdb_00009rxm

Cryo-EM structure of TCRpriv/pMHC

• PDB DOI: https://doi.org/10.2210/pdb9RXM/pdb
• EM Map EMD-54366: EMDB EMDataResource

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


• Deposited: 2025-07-11 Released: 2025-08-13 
• Deposition Author(s): Akil, C., Zhu, Y., Hardenbrook, N., Zhang, P.
• Funding Organization(s): Chinese Academy of Sciences, Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of TCRpriv/pMHC

Akil, C., Zhu, Y., Hardenbrook, N., Zhang, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 94.67 kDa 
• Atom Count: 6,063 
• Modeled Residue Count: 752 
• Deposited Residue Count: 827 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha chain	A	205	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta chain	B	242	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 ORF3a_207-215 epitope	C [auth D]	9	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	D [auth E]	272	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A7WPI8 (Homo sapiens) Explore A7WPI8  Go to UniProtKB:  A7WPI8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	E [auth F]	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	5

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Akil, C., Zhu, Y., Hardenbrook, N., Zhang, P.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	2024-I2M-2-001-1
Wellcome Trust	United Kingdom	203141/Z/16/Z

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release