25RG | pdb_000025rg

CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS045

PDB DOI: https://doi.org/10.2210/pdb25RG/pdb
EM Map EMD-80320: EMDB EMDataResource

Classification: TOXIN/IMMUNE SYSTEM
Organism(s): Shigella dysenteriae, Homo sapiens
Expression System: Escherichia coli, Cricetulus griseus
Mutation(s): No

Deposited: 2026-04-15 Released: 2026-09-02
Deposition Author(s): Chen, S.D., Li, X.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Resolution: 2.50 Å
Resolution: 2.50 Å
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 25RG

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

Literature

CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising RDS045(pentamer)

Chen, S.D., Li, X.

To be published.

Macromolecule Content

Total Structure Weight: 275.78 kDa
Atom Count: 19,365
Modeled Residue Count: 2,545
Deposited Residue Count: 2,545
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiga toxin subunit B	A, D, G [auth E], J [auth F], M [auth G]	73	Shigella dysenteriae	Mutation(s): 0 Gene Names: stxB, SDY_1390
UniProt
Find proteins for Q32GM0 (Shigella dysenteriae serotype 1 (strain Sd197)) Explore Q32GM0 Go to UniProtKB: Q32GM0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32GM0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of RDS045 Fab	B, E [auth H], H [auth I], K [auth J], N [auth K]	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of RDS045 Fab	C, F [auth L], I [auth M], L [auth N], O	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Resolution: 2.50 Å
Resolution: 2.50 Å
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-09-02
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.