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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9RXM

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of TCRpriv/pMHC

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

To be published.

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

Find similar proteins by:

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

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

Find similar proteins by: Sequence | 3D Structure

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7WPI8
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Hardenbrook, N.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.