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- EMDB-48780: Cryo-EM of spore appendage from Anaerovoracaceae -

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Basic information

Entry
Database: EMDB / ID: EMD-48780
TitleCryo-EM of spore appendage from Anaerovoracaceae
Map datacryo-EM of spore appendages from Anaerovoracaceae
Sample
  • Complex: spore appendage
    • Protein or peptide: spore filament protein subunit
Keywordsspore appendage / helical filament / protein polymer / helical / PROTEIN FIBRIL
Biological speciesBacillota bacterium (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBellis NF / Baquero DP / Egelman EH / Krupovic M / Wang F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM identifies F-ENA of Bacillus thuringiensis as a widespread family of endospore appendages across Firmicutes.
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, Bacillus thuringiensis (Bt) has been used as an agricultural biopesticide to control pests caused by insect species in the orders of Lepidoptera, Diptera, and Coleoptera. Under ...For over 100 years, Bacillus thuringiensis (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, 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 filaments anchored to the exosporium and tipped with a flexible fibrillum. Phylogenetic and structural analyses reveal that F-ENA are conserved in Bacilli and Clostridia, featuring head-neck domains with β-barrel necks that interlock via N-terminal hook peptides. In Bacillus, two collagen-like proteins (F-Anchor and F-BclA), respectively, tether F-ENA and form the distal tip. Sedimentation assays suggest F-ENA promotes spore clustering via F-BclA contacts and/or filament bundling.
History
DepositionJan 23, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48780.png

Downloads & links

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Map

FileDownload / File: emd_48780.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM of spore appendages from Anaerovoracaceae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.27
Minimum - Maximum0.0 - 9.579727
Average (Standard dev.)0.038086094 (±0.32819512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_48780_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_48780_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : spore appendage

EntireName: spore appendage
Components
  • Complex: spore appendage
    • Protein or peptide: spore filament protein subunit

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Supramolecule #1: spore appendage

SupramoleculeName: spore appendage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillota bacterium (bacteria)

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Macromolecule #1: spore filament protein subunit

MacromoleculeName: spore filament protein subunit / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Bacillota bacterium (bacteria)
Molecular weightTheoretical: 13.182613 KDa
SequenceString:
MATSLFKLVM SATTSTTTDT NPEVERYFYR LNPAQRTSGT LTIPSTSFTN SSGAAVTSNI VTAATDNGYY LLFINGAFQE TSLFTVAAS QVRITQTSLV PTSAPITLVV NNFAPTSTST TTVRS

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: 71.17 Å
Applied symmetry - Helical parameters - Δ&Phi: 74.43 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40641
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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