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- PDB-9sjb: Solution structure of Clostridioides difficile CspB oligomer dete... -

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Basic information

Entry
Database: PDB / ID: 9sjb
TitleSolution structure of Clostridioides difficile CspB oligomer determined by CryoEM
Components(Subtilisin-like serine germination related protease) x 2
KeywordsHYDROLASE / Protease / Clostridium / spore germination / oligomer
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / :
Similarity search - Function
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
Subtilisin-like serine germination related protease
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsAlcorlo, M. / Lazaro, M. / Valle, 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 oligomer determined by CryoEM
Authors: Alcorlo, M. / Hermoso, J.
History
DepositionAug 31, 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: Subtilisin-like serine germination related protease
B: Subtilisin-like serine germination related protease
C: Subtilisin-like serine germination related protease
D: Subtilisin-like serine germination related protease
E: Subtilisin-like serine germination related protease
F: Subtilisin-like serine germination related protease
G: Subtilisin-like serine germination related protease
H: Subtilisin-like serine germination related protease
I: Subtilisin-like serine germination related protease
J: Subtilisin-like serine germination related protease
K: Subtilisin-like serine germination related protease
L: Subtilisin-like serine germination related protease
LL: Subtilisin-like serine germination related protease
M: Subtilisin-like serine germination related protease
N: Subtilisin-like serine germination related protease
O: Subtilisin-like serine germination related protease
P: Subtilisin-like serine germination related protease
Q: Subtilisin-like serine germination related protease
R: Subtilisin-like serine germination related protease
S: Subtilisin-like serine germination related protease
T: Subtilisin-like serine germination related protease
V: Subtilisin-like serine germination related protease
W: Subtilisin-like serine germination related protease
X: Subtilisin-like serine germination related protease
Y: Subtilisin-like serine germination related protease
Z: Subtilisin-like serine germination related protease
YY: Subtilisin-like serine germination related protease
ZZ: Subtilisin-like serine germination related protease
AA: Subtilisin-like serine germination related protease
BB: Subtilisin-like serine germination related protease
CC: Subtilisin-like serine germination related protease
EE: Subtilisin-like serine germination related protease
FF: Subtilisin-like serine germination related protease
GG: Subtilisin-like serine germination related protease


Theoretical massNumber of molelcules
Total (without water)1,010,05234
Polymers1,010,05234
Non-polymers00
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
Subtilisin-like serine germination related protease


Mass: 7796.887 Da / Num. of mol.: 18
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
#2: Protein
Subtilisin-like serine germination related protease


Mass: 54356.773 Da / Num. of mol.: 16
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
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: CspB protase in complex with its prodomain forming an oligomeric structure
Type: COMPLEX / Entity ID: #2, #1 / 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
5CTFFINDCTF correction
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 135.9 ° / Axial rise/subunit: 24.7 Å / Axial symmetry: C1
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 200 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 85.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003468388
ELECTRON MICROSCOPYf_angle_d0.601893012
ELECTRON MICROSCOPYf_chiral_restr0.048110827
ELECTRON MICROSCOPYf_plane_restr0.003512080
ELECTRON MICROSCOPYf_dihedral_angle_d5.07439346

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