9RT4 | pdb_00009rt4

NetF - ANTXR2 local refinement focused

PDB DOI: https://doi.org/10.2210/pdb9RT4/pdb
EM Map EMD-54245: EMDB EMDataResource

Classification: TOXIN
Organism(s): Homo sapiens, Clostridium perfringens
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2025-07-02 Released: 2026-02-18
Deposition Author(s): Wang, C., Iacovache, I., Zuber, B.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9RT4

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

Literature

Anthrax toxin receptor 2 is the Receptor for Clostridium perfringens NetF: Structural Insights into Toxin Binding and Pore Formation

Wang, C., Cattalani, F., Iacovache, I., Arunasalam, N., Posthaus, H., Zuber, B.

To be published.

Macromolecule Content

Total Structure Weight: 71.64 kDa
Atom Count: 3,016
Modeled Residue Count: 387
Deposited Residue Count: 645
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthrax toxin receptor 2	A [auth C1]	356	Homo sapiens	Mutation(s): 0 Gene Names: ANTXR2, CMG2
UniProt & NIH Common Fund Data Resources
Find proteins for P58335 (Homo sapiens) Explore P58335 Go to UniProtKB: P58335
PHAROS: P58335 GTEx: ENSG00000163297
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P58335
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocidin/Hemolysin toxin family	B [auth N2]	289	Clostridium perfringens	Mutation(s): 0 Gene Names: netF, JFP838_pC0069
UniProt
Find proteins for A0A0D3QGV4 (Clostridium perfringens) Explore A0A0D3QGV4 Go to UniProtKB: A0A0D3QGV4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0D3QGV4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	10000175

Revision History (Full details and data files)

Version 1.0: 2026-02-18
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.