9RUP | pdb_00009rup

Cryo-EM structure of TCRpub/pMHC dimer

• PDB DOI: https://doi.org/10.2210/pdb9RUP/pdb
• EM Map EMD-54273: EMDB EMDataResource

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


• Deposited: 2025-07-04 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: 4.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of TCRpub/pMHC dimer

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 190.37 kDa 
• Atom Count: 12,807 
• Modeled Residue Count: 1,596 
• Deposited Residue Count: 1,670 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor, alpha chain	A, F [auth a]	209	Homo sapiens	Mutation(s): 0

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	C [auth E], H [auth e]	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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	D [auth C], I [auth c]	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A0D6K978 (Homo sapiens) Explore A0A0D6K978  Go to UniProtKB:  A0A0D6K978

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF3a_207-215 epitope	E [auth D], J [auth d]	9	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

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