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- PDB-9sj9: Solution structure of Clostridioides difficile CspA protein in co... -

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Basic information

Entry
Database: PDB / ID: 9sj9
TitleSolution structure of Clostridioides difficile CspA protein in complex with CspC and Taurocholate, determined by CryoEM
Components
  • S8 family peptidase
  • Subtilisin-like serine germination related protease
KeywordsSIGNALING PROTEIN / Pseudo Protease / Clostridium / spore germination / taurocholate
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / :
Similarity search - Function
Peptidase S8A, subtilisin-related, clostridia / Csp protease B, prodomain / Csp protease B prodomain / CspA-like domain / : / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily ...Peptidase S8A, subtilisin-related, clostridia / Csp protease B, prodomain / Csp protease B prodomain / CspA-like domain / : / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
TAUROCHOLIC ACID / S8 family peptidase / Subtilisin-like serine germination related protease
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsAlcorlo, M. / Hermoso, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-153118OB-I00 Spain
CitationJournal: To Be Published
Title: Solution structure of Clostridioides difficile CspB protein determined by CryoEM
Authors: Alcorlo, M. / Hermoso, J.
History
DepositionAug 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S8 family peptidase
B: Subtilisin-like serine germination related protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0285
Polymers126,4812
Non-polymers1,5473
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein S8 family peptidase / Subtilisin-like serine germination related protease


Mass: 61601.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: cspC, cspC_2, BN1095_330133, KRM00_001799, SAMEA1402399_00500
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A031WJ37
#2: Protein Subtilisin-like serine germination related protease


Mass: 64879.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cspBA, SAMEA1402399_00499
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0AB74Q767, subtilisin
#3: Chemical ChemComp-TCH / TAUROCHOLIC ACID


Mass: 515.703 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H45NO7S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CspA in complex with CspC an taurocholate / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Clostridioides difficile (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: ice
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.03 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8258331
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1105013 / Symmetry type: POINT
RefinementHighest resolution: 2.75 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038807
ELECTRON MICROSCOPYf_angle_d0.55412015
ELECTRON MICROSCOPYf_dihedral_angle_d5.8171285
ELECTRON MICROSCOPYf_chiral_restr0.0471396
ELECTRON MICROSCOPYf_plane_restr0.0041539

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