9SJ6 | pdb_00009sj6

Structure of the Clostridioides difficile CspB protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.258 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9SJ6

This is version 1.1 of the entry. See complete history

Literature

Structure of core assembly of the Clostridioides difficile germinosome.

Cal Y Mayor Luna, C.Alcorlo, M.Kim, C.Jacobson, G.N.Lazaro, M.Valle, M.Chang, M.Hermoso, J.A.Mobashery, S.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-74264-w
  • Primary Citation Related Structures: 
    9SJ6

  • PubMed Abstract: 

    The germinosome is the machinery of Clostridioides difficile that sets in motion the process of spore germination to vegetative bacteria. Three highly-regulated proteins-CspA, CspB and CspC-serve as key instigators of germination. We report that CspA and CspB exist independently as homodimers in solution. In the presence of CspC, a picomolar complex of CspA:CspC forms. Furthermore, we document that CspA binds to the germinant, taurocholate, and that the complex CspA:CspC:taurocholate serves as the receptor for glycine, the co-germinant. We report high-resolution X-ray and cryo-EM structures for the three proteins, and for the CspA:CspC:taurocholate complex. These structures show how the CspA:CspC heterodimer recognizes taurocholate and reveal that specific structural features in the three Csp proteins avoid the recognition of the germinant by homodimers. Remarkably, the homodimer of CspB organizes itself in a supramolecular fibril assembly comprised of a three-stranded right-handed superhelix. These proteins are targets for interference with the transition from spore to the vegetative form of C. difficile.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.

Macromolecule Content 

  • Total Structure Weight: 123.73 kDa 
  • Atom Count: 8,535 
  • Modeled Residue Count: 1,062 
  • Deposited Residue Count: 1,114 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Subtilisin-like serine germination related protease
A, B
65Clostridioides difficileMutation(s): 0 
Gene Names: cspBABN1096_520472
UniProt
Find proteins for A0A069A4Z2 (Clostridioides difficile)
Explore A0A069A4Z2 
Go to UniProtKB:  A0A069A4Z2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A069A4Z2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Subtilisin-like serine germination related protease
C, D
492Clostridioides difficileMutation(s): 0 
Gene Names: cspBASAMEA1402399_00499
EC: 3.4.21.62
UniProt
Find proteins for A0AB74Q767 (Clostridioides difficile)
Explore A0AB74Q767 
Go to UniProtKB:  A0AB74Q767
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AB74Q767
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.258 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.909α = 90
b = 115.726β = 90
c = 201.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2023-153118OB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-17
    Type: Initial release
  • Version 1.1: 2026-07-01
    Changes: Database references