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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9RUP

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

Literature

Cryo-EM structure of TCRpub/pMHC dimer

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

To be published.

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

Find similar proteins by:

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

Find similar proteins by:

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

Find similar proteins by:

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0D6K978
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.