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)

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Experimental Data Snapshot

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

Literature

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

Yao, Z., Xiechao, Z., Liang, T.

(2023) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Zhan, X., Tao, L.

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

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Structure summary