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- EMDB-54941: Solution structure of Clostridioides difficile CspA protein in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-54941
TitleSolution structure of Clostridioides difficile CspA protein in complex with CspC and Taurocholate, determined by CryoEM
Map data
Sample
  • Complex: CspA in complex with CspC an taurocholate
    • Protein or peptide: S8 family peptidase
    • Protein or peptide: Subtilisin-like serine germination related protease
  • Ligand: TAUROCHOLIC ACID
KeywordsPseudo Protease / Clostridium / spore germination / taurocholate / SIGNALING PROTEIN
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
S8 family peptidase / Subtilisin-like serine germination related protease
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsAlcorlo 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 protein determined by CryoEM
Authors: Alcorlo M / Hermoso J
History
DepositionAug 30, 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_54941.png

Downloads & links

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Map

FileDownload / File: emd_54941.map.gz / Format: CCP4 / Size: 30.5 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 200 pix.
= 168. Å		0.84 Å/pix.
x 200 pix.
= 168. Å		0.84 Å/pix.
x 200 pix.
= 168. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00781
Minimum - Maximum-0.021580188 - 0.046051066
Average (Standard dev.)0.00009102067 (±0.0019178363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 168.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54941_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54941_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 : CspA in complex with CspC an taurocholate

EntireName: CspA in complex with CspC an taurocholate
Components
  • Complex: CspA in complex with CspC an taurocholate
    • Protein or peptide: S8 family peptidase
    • Protein or peptide: Subtilisin-like serine germination related protease
  • Ligand: TAUROCHOLIC ACID

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Supramolecule #1: CspA in complex with CspC an taurocholate

SupramoleculeName: CspA in complex with CspC an taurocholate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Clostridioides difficile (bacteria)

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Macromolecule #1: S8 family peptidase

MacromoleculeName: S8 family peptidase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 61.601645 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MEKSYCIIYQ GDIESALQEN GINRYMVLNS QLAVIYVPLD FDETILNNII QVAWWEESEP MSSLIEITNN VNNGETITTA AETDYIYEN PYNDITGRGI LLAVIDSGID YLHPDFINDD GTSKVLYLWD QEANTNPPPE GFIFGSEFTR SELNIAINRN D GSLSQDNI ...String:
MEKSYCIIYQ GDIESALQEN GINRYMVLNS QLAVIYVPLD FDETILNNII QVAWWEESEP MSSLIEITNN VNNGETITTA AETDYIYEN PYNDITGRGI LLAVIDSGID YLHPDFINDD GTSKVLYLWD QEANTNPPPE GFIFGSEFTR SELNIAINRN D GSLSQDNI GTGTLVSGIL VGNGRINSQY RGITTESDLI VVKLKSYTDT YYAGRINYSV SDFLAAITYV TNIARTENKP LI INLTIGV KSSAVATTSI LDTFNILSSA GVVVVSGAGN QGNTDIHYSG RFSSVGEVQD VIIQDGDDYA LDITLNTNGP DKV GAQIIS PSGEVSHDIR YSPDFYIYRG KFNLENTTYA MRFIYPYITS GKENLEIRLR DIKPGVWILR LTSELIINGE YDIY LPNKN LIAPDTRFLD PDSVATITMY AASDDVITVG TFNNKTDSMW IGSSKGPIRG RGIKPDIVAS GVDIISTYKN GTYNT GTGT GVSSSIVTGV LALLMEYLEK QDNVPRLSLF TQVLKTYLIL GATKLEIYTY PNVSQGYGIL NLKNTIQQIA NTLEL

UniProtKB: S8 family peptidase

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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: 1 / Enantiomer: LEVO / EC number: subtilisin
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 64.879336 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGFKDEENSY KFIDGYNMQI HNDLENEIYI SKNASRQSGI LSGIDIVHTP EFEEELAGLG MSQRFFKISD SLGVLSINNT DYSSIQRVL QLPSIIRTVS TTKMTLLGEI NRGTFGGVVA TEEMGVNFFK NNPNINITGR GTLISIADTG IDYLHPDFIY P DGTSKIVY ...String:
MGFKDEENSY KFIDGYNMQI HNDLENEIYI SKNASRQSGI LSGIDIVHTP EFEEELAGLG MSQRFFKISD SLGVLSINNT DYSSIQRVL QLPSIIRTVS TTKMTLLGEI NRGTFGGVVA TEEMGVNFFK NNPNINITGR GTLISIADTG IDYLHPDFIY P DGTSKIVY LWDQTKEGTP PDGFYIGTEY TREDINRAIA ENDPSLSQDE VGQGTMLSGI CAGLGNVNSE YAGIAEDSEL II IKLGKID DFYNSAMLFA ASQYAYKKAF ELGRPLVINM SLGTSSLAGL TNRSNSEKAF FTRGLCITAG AGNEGNTQTH TSG IIPYVG GSVEVELELN EDEEELSLEL WLNRPDKADV IIVSPTGEES KSVGISNYNK VTGLFDLEGT EYSITYIYPT TFSG QQFTN VTLKNAKRGV WKIRLVGVYI ITGRYNLYLP NRELLKSGTR FREVDPFYTI NYPAIQDDLI TIGAYNTING SLWQS SSRG PTIEDRLKPD IVAPGVNIIA AYPGNTYATI TGTAAASAHA AGAAAMYFQY TFVDGRYPNQ AYVQKIKTFM QAGARK DSN TVYPNTNSGY GLLDVRGMFD VLRLDAL

UniProtKB: Subtilisin-like serine germination related protease

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Macromolecule #3: TAUROCHOLIC ACID

MacromoleculeName: TAUROCHOLIC ACID / type: ligand / ID: 3 / Number of copies: 3 / Formula: TCH
Molecular weightTheoretical: 515.703 Da
Chemical component information

ChemComp-TCH:
TAUROCHOLIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle 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

Particle selectionNumber selected: 8258331
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Initial model obtained with Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 1105013
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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