8Y9B

TcdB1 in complex with mini-binder

• PDB DOI: https://doi.org/10.2210/pdb8Y9B/pdb
• EM Map EMD-39072: EMDB EMDataResource

• Classification: TOXIN/DE NOVO PROTEIN
• Organism(s): Clostridioides difficile, synthetic construct
• Expression System: Bacillus subtilis, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-06 Released: 2024-08-28 
• Deposition Author(s): Lv, X.C., Lu, P.L.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental

Literature

TcdB1 in complex with mini-binder

Lv, X.C., Lu, P.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 278.27 kDa 
• Atom Count: 13,380 
• Modelled Residue Count: 1,672 
• Deposited Residue Count: 2,437 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin B	A [auth B]	2,372	Clostridioides difficile	Mutation(s): 0  Gene Names: tcdB, toxB EC: 3.4.22
UniProt
Find proteins for P18177 (Clostridioides difficile) Explore P18177  Go to UniProtKB:  P18177

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo design mini-binder	B [auth A]	65	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Lv, X.C., Lu, P.L.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFA0909200
National Natural Science Foundation of China (NSFC)	China	32301219

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release