9SJB | pdb_00009sjb

Solution structure of Clostridioides difficile CspB oligomer determined by CryoEM

• PDB DOI: https://doi.org/10.2210/pdb9SJB/pdb
• EM Map EMD-54942: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-08-31 Released: 2026-06-17 
• Deposition Author(s): Alcorlo, M., Lazaro, M., Valle, M., Hermoso, J.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: HELICAL 

Literature

Solution structure of Clostridioides difficile CspB oligomer determined by CryoEM

Alcorlo, M., Hermoso, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 34-mer - A18B16 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,010.05 kDa 
• Atom Count: 67,110 
• Modeled Residue Count: 8,615 
• Deposited Residue Count: 9,096 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin-like serine germination related protease	A, B, CA [auth AA], DA [auth BB], E, F, FA [auth EE], GA [auth FF], I, J, M [auth LL], N [auth M], Q [auth P], R [auth Q], U [auth T], V, Y, Z	68	Clostridioides difficile	Mutation(s): 0  Gene Names: cspBA, SAMEA1402399_00499 EC: 3.4.21.62
UniProt
Find proteins for A0AB74Q767 (Clostridioides difficile) Explore A0AB74Q767  Go to UniProtKB:  A0AB74Q767

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin-like serine germination related protease	AA [auth YY], BA [auth ZZ], C, D, EA [auth CC], G, H, HA [auth GG], K, L, O [auth N], P [auth O], S [auth R], T [auth S], W, X	492	Clostridioides difficile	Mutation(s): 0  Gene Names: cspBA, SAMEA1402399_00499 EC: 3.4.21.62
UniProt
Find proteins for A0AB74Q767 (Clostridioides difficile) Explore A0AB74Q767  Go to UniProtKB:  A0AB74Q767

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-17 
Deposition Author(s): Alcorlo, M., Lazaro, M., Valle, M., Hermoso, J.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2023-153118OB-I00

Revision History  

• Version 1.0: 2026-06-17
  Type: Initial release