8JB5 | pdb_00008jb5

The cryo-EM structure of Paeniclostridium sordellii lethal toxin (TcsL)

PDB DOI: https://doi.org/10.2210/pdb8JB5/pdb
EM Map EMD-36141: EMDB EMDataResource

Classification: TOXIN
Organism(s): Paraclostridium sordellii ATCC 9714
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2023-05-08 Released: 2023-12-13
Deposition Author(s): Zhan, X., Tao, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8JB5

This is version 1.2 of the entry. See complete history.

Literature

Structural dynamics of CROPs control stability and toxicity of Paeniclostridium sordellii lethal toxin

Yao, Z., Xiechao, Z., Liang, T.

(2023) Nat Commun

Macromolecule Content

Total Structure Weight: 271.89 kDa
Atom Count: 19,027
Modeled Residue Count: 2,355
Deposited Residue Count: 2,372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxin-L	A	2,372	Paraclostridium sordellii ATCC 9714	Mutation(s): 0 Gene Names: tcsL, H477_0263 EC: 3.4.22
UniProt
Find proteins for T0D3N5 (Paraclostridium sordellii (strain ATCC 9714 / DSM 2141 / JCM 3814 / LMG 15708 / NCIMB 10717 / 211)) Explore T0D3N5 Go to UniProtKB: T0D3N5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T0D3N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Structure summary
Version 1.2: 2025-07-23
Changes: Data collection, Structure summary

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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.