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- EMDB-54942: Solution structure of Clostridioides difficile CspB oligomer dete... -

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Basic information

Entry
Database: EMDB / ID: EMD-54942
TitleSolution structure of Clostridioides difficile CspB oligomer determined by CryoEM
Map data
Sample
  • Complex: CspB protase in complex with its prodomain forming an oligomeric structure
    • Protein or peptide: Subtilisin-like serine germination related protease
    • Protein or peptide: Subtilisin-like serine germination related protease
KeywordsProtease / Clostridium / spore germination / oligomer / HYDROLASE
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)
Methodhelical reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsAlcorlo M / Lazaro M / Valle M / Hermoso J
Funding support Spain, 1 items
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, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54942.png

Downloads & links

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Map

FileDownload / File: emd_54942.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 318 pix.
= 266.802 Å		0.84 Å/pix.
x 318 pix.
= 266.802 Å		0.84 Å/pix.
x 318 pix.
= 266.802 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0135
Minimum - Maximum-0.025420438 - 0.053435344
Average (Standard dev.)0.000106528554 (±0.0028315387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions318318318
Spacing318318318
CellA=B=C: 266.802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54942_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54942_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CspB protase in complex with its prodomain forming an oligomeric ...

EntireName: CspB protase in complex with its prodomain forming an oligomeric structure
Components
  • Complex: CspB protase in complex with its prodomain forming an oligomeric structure
    • Protein or peptide: Subtilisin-like serine germination related protease
    • Protein or peptide: Subtilisin-like serine germination related protease

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Supramolecule #1: CspB protase in complex with its prodomain forming an oligomeric ...

SupramoleculeName: CspB protase in complex with its prodomain forming an oligomeric structure
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Clostridioides difficile (bacteria)

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Macromolecule #1: Subtilisin-like serine germination related protease

MacromoleculeName: Subtilisin-like serine germination related protease / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO / EC number: subtilisin
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 7.796887 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MIIINYELIV KYNGDILRLE EELGVSVEIL NSSYAIITSS NEEDVNILLT YPEIEFIEKP FILQTCSP

UniProtKB: Subtilisin-like serine germination related protease

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Macromolecule #2: Subtilisin-like serine germination related protease

MacromoleculeName: Subtilisin-like serine germination related protease / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO / EC number: subtilisin
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 54.356773 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MQDVQSFSST GITGFKNRTG LTGKGTIIGI IDSGIDYTLP VFRDSDGRSK ILYYWDQSIQ GNPPEGFREG TLYTNEDINN AIDGSMYIP ISTTSLHGTH VAGICATIAS DARIIVVRVG NIQTDIFSRS TEFMRAIKFI LDRALELRMP VTLNISYGSN E GSHRGTSL ...String:
MQDVQSFSST GITGFKNRTG LTGKGTIIGI IDSGIDYTLP VFRDSDGRSK ILYYWDQSIQ GNPPEGFREG TLYTNEDINN AIDGSMYIP ISTTSLHGTH VAGICATIAS DARIIVVRVG NIQTDIFSRS TEFMRAIKFI LDRALELRMP VTLNISYGSN E GSHRGTSL FEQYIDDMCL FWKNNIVVAA GNNADKGGHK RIRLQNNITE EVEFIVGEGE RILNINIWPD FVDDFSVHLV NP SNNQTQA ISLTSGEIRN TLGETRITGY FYPIAPYSLT RRVTLQLSSN TQITPGLWKI VFEPIDIVTG NVNIYLPTSE GLN RNTRFL IPTQELTVTV PGTASRVITV GSFNSRTDIV SIFSGEGDTQ LGVFKPDLLA PGEDIVSFLP GGTSGALTGT SMAT PHVTG VCSLFMEWGI VNGNDLFLYS QKLRALLLKG ARRLSNQSYP NNSSGFGFLN LSDIDLYTLS NINQDLETED MGYRS INKS LEHHHHHH

UniProtKB: Subtilisin-like serine germination related protease

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Sugar embeddingMaterial: ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 24.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 135.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 200
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Initial model obtained with Relion
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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