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- EMDB-52523: CryoEM structure of F-ENA fibers on the spores of Bacillus thurin... -

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Basic information

Entry
Database: EMDB / ID: EMD-52523
TitleCryoEM structure of F-ENA fibers on the spores of Bacillus thuringiensis serovar kurstaki
Map data
Sample
  • Complex: F-ENA
    • Protein or peptide: DUF4183 domain-containing protein
KeywordsENA / endospore appendage / protein fiber / helical / PROTEIN FIBRIL
Function / homology:
Function and homology information
Biological speciesBacillus thuringiensis serovar kurstaki (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsSleutel M / Remaut H
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G043021N Belgium
CitationJournal: bioRxiv / Year: 2025
Title: Cryo-EM analysis of the extrasporal matrix identifies F-ENA as a widespread family of endospore appendages across the Firmicutes phylum.
Authors: Mike Sleutel / Adrià Sogues / Nani Van Gerven / Unni Lise Jonsmoen / Inge Van Molle / Marcus Fislage / Laurent Dirk Theunissen / Nathan F Bellis / Diana P Baquero / Edward H Egelman / Mart ...Authors: Mike Sleutel / Adrià Sogues / Nani Van Gerven / Unni Lise Jonsmoen / Inge Van Molle / Marcus Fislage / Laurent Dirk Theunissen / Nathan F Bellis / Diana P Baquero / Edward H Egelman / Mart Krupovic / Fengbin Wang / Marina Aspholm / Han Remaut /
Abstract: For over 100 years, (Bt) has been used as an agricultural biopesticide to control pests caused by insect species in the orders of Lepidoptera, Diptera and Coleoptera. Under nutrient starvation, Bt ...For over 100 years, (Bt) has been used as an agricultural biopesticide to control pests caused by insect species in the orders of Lepidoptera, Diptera and Coleoptera. Under nutrient starvation, Bt cells differentiate into spores and associated toxin crystals that can adopt biofilm-like aggregates. We reveal that such Bt spore/toxin biofilms are embedded in a fibrous extrasporal matrix (ESM), and using cryoID, we resolved the structure and molecular identity of an uncharacterized type of pili, referred to here as Fibrillar ENdospore Appendages or 'F-ENA'. F-ENA are monomolecular protein polymers tethered to the exosporium of Bt and are decorated with a flexible tip fibrillum. Phylogenetic analysis reveals that F-ENA is widespread not only in the class Bacilli, but also in the class Clostridia, and the cryoEM structures of F-ENA filaments from and reveal subunits with a generic head-neck domain structure, where the β-barrel neck of variable length latch onto a preceding head domain through short N-terminal hook peptides. In , two collagen-like proteins (CLP) respectively tether F-ENA to the exosporium (F-Anchor), or constitute the tip fibrillum at the distal terminus of F-ENA (F-BclA). Sedimentation assays point towards F-ENA involvement in spore-spore clustering, likely mediated via F-BclA contacts and F-ENA bundling through the antiparallel interlocking of the head-neck units.
History
DepositionJan 13, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52523.png

Downloads & links

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Map

FileDownload / File: emd_52523.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å

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Voxel sizeX=Y=Z: 1.39 Å
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Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.03221467 - 0.2094212
Average (Standard dev.)0.00057370414 (±0.006700295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 355.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52523_msk_1.map
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Additional map: #1

Fileemd_52523_additional_1.map
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Half map: #2

Fileemd_52523_half_map_1.map
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Half map: #1

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Sample components

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Entire : F-ENA

EntireName: F-ENA
Components
  • Complex: F-ENA
    • Protein or peptide: DUF4183 domain-containing protein

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Supramolecule #1: F-ENA

SupramoleculeName: F-ENA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus thuringiensis serovar kurstaki (bacteria)
Molecular weightTheoretical: 8.627 kDa/nm

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Macromolecule #1: DUF4183 domain-containing protein

MacromoleculeName: DUF4183 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thuringiensis serovar kurstaki (bacteria)
Molecular weightTheoretical: 9.692923 KDa
Recombinant expressionOrganism: Bacillus thuringiensis serovar kurstaki (bacteria)
SequenceString:
MPIIQPFMAS RRFTSTLGAG TGTGAAFAIA ATACLNDAGT TATAFPTFTY YNLYVNGILQ PSVNSSVTTG PTGAITIPGG DALDGGIPI TIEFIVT

UniProtKB: UNIPROTKB: A0AAX0C6N4

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 33.54 Å
Applied symmetry - Helical parameters - Δ&Phi: 42.73 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 196540
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold3
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9hze:
CryoEM structure of F-ENA fibers on the spores of Bacillus thuringiensis serovar kurstaki

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