1UYJ | pdb_00001uyj

Clostridium perfringens epsilon toxin shows structural similarity with the pore forming toxin aerolysin

PDB DOI: https://doi.org/10.2210/pdb1UYJ/pdb

Classification: TOXIN
Organism(s): Clostridium perfringens
Mutation(s): No

Deposited: 2004-03-02 Released: 2004-08-05
Deposition Author(s): Cole, A.R., Gibert, M., Poppoff, M., Moss, D.S., Titball, R.W., Basak, A.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.290 (Depositor), 0.240 (DCC)
R-Value Work:
0.236 (Depositor), 0.241 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Clostridium Perfringens Epsilon-Toxin Shows Structural Similarity to the Pore-Forming Toxin Aerolysin

Cole, A.R., Gibert, M., Popoff, M., Moss, D.S., Titball, R.W., Basak, A.K.

(2004) Nat Struct Mol Biol 11: 797

PubMed: 15258571 Search on PubMed
DOI: https://doi.org/10.1038/nsmb804
Primary Citation Related Structures:
1UYJ

PubMed Abstract:
Epsilon-toxin from Clostridium perfringens is a lethal toxin. Recent studies suggest that the toxin acts via an unusually potent pore-forming mechanism. Here we report the crystal structure of epsilon-toxin, which reveals structural similarity to aerolysin from Aeromonas hydrophila. Pore-forming toxins can change conformation between soluble and transmembrane states. By comparing the two toxins, we have identified regions important for this transformation.

Organizational Affiliation

Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.

Macromolecule Content

Total Structure Weight: 101.9 kDa
Atom Count: 6,320
Modeled Residue Count: 819
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPSILON-TOXIN	A, B, C	296	Clostridium perfringens	Mutation(s): 0
UniProt
Find proteins for Q57398 (Clostridium perfringens) Explore Q57398 Go to UniProtKB: Q57398
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q57398
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U1 Query on U1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain L [auth C] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] G [auth B] H [auth B] D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C]	URANIUM ATOM U JFALSRSLKYAFGM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.290 (Depositor), 0.240 (DCC)
R-Value Work: 0.236 (Depositor), 0.241 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.962	α = 90
b = 125.962	β = 90
c = 121.862	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
SHARP	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-08-05
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other

1UYJ | pdb_00001uyj

Clostridium perfringens epsilon toxin shows structural similarity with the pore forming toxin aerolysin

Literature

Clostridium Perfringens Epsilon-Toxin Shows Structural Similarity to the Pore-Forming Toxin Aerolysin

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand