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- EMDB-17627: Recombinant Ena3A L-Type endospore appendages -

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Basic information

Entry
Database: EMDB / ID: EMD-17627
TitleRecombinant Ena3A L-Type endospore appendages
Map data
Sample
  • Organelle or cellular component: Recombinant Ena3A L-type endospore appendage
    • Protein or peptide: DUF3992 domain-containing protein
KeywordsEndospore / Pili / Protein / Fiber / Spore / Appendage / Bacillus paranthracis / PROTEIN FIBRIL / recombinant
Function / homologyEndospore appendages core / Endospore appendages / Endospore appendages core domain-containing protein
Function and homology information
Biological speciesBacillus paranthracis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsSleutel M / Remaut H
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
Citation
Journal: Nat Commun / Year: 2024
Title: Helical ultrastructure of the L-ENA spore aggregation factor of a Bacillus paranthracis foodborne outbreak strain.
Authors: Mike Sleutel / Ephrem Debebe Zegeye / Ann-Katrin Llarena / Brajabandhu Pradhan / Marcus Fislage / Kristin O'Sullivan / Nani Van Gerven / Marina Aspholm / Han Remaut /
Abstract: In pathogenic Bacillota, spores can form an infectious particle and can take up a central role in the environmental persistence and dissemination of disease. A poorly understood aspect of spore- ...In pathogenic Bacillota, spores can form an infectious particle and can take up a central role in the environmental persistence and dissemination of disease. A poorly understood aspect of spore-mediated infection is the fibrous structures or 'endospore appendages' (ENAs) that have been seen to decorate the spores of pathogenic Bacilli and Clostridia. Current methodological approaches are opening a window on these long enigmatic structures. Using cryoID, Alphafold modelling and genetic approaches we identify a sub-class of robust ENAs in a Bacillus paranthracis foodborne outbreak strain. We demonstrate that L-ENA are encoded by a rare three-gene cluster (ena3) that contains all components for the self-assembly of ladder-like protein nanofibers of stacked heptameric rings, their anchoring to the exosporium, and their termination in a trimeric 'ruffle' made of a complement C1Q-like BclA paralogue. The role of ENA fibers in spore-spore interaction and the distribution of L-ENA operon as mobile genetic elements in B. cereus s.l. strains suggest that L-ENA fibers may increase the survival, spread and virulence of these strains.
#1: Journal: Biorxiv / Year: 2023
Title: A novel class of ultra-stable endospore appendages decorated with collagen-like tip fibrillae
Authors: Sleutel M / Zegeye ED / Llarena AK / Pradhan B / Fislage M / O'Sullivan K / Aspholm M / Remaut H
History
DepositionJun 13, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17627.png

Downloads & links

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Map

FileDownload / File: emd_17627.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 300 pix.
= 229.2 Å		0.76 Å/pix.
x 300 pix.
= 229.2 Å		0.76 Å/pix.
x 300 pix.
= 229.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.764 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0913
Minimum - Maximum-0.023489663 - 0.23726764
Average (Standard dev.)0.004084828 (±0.019951204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 229.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17627_msk_1.map
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Half map: #2

Fileemd_17627_half_map_1.map
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Half map: #1

Fileemd_17627_half_map_2.map
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Sample components

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Entire : Recombinant Ena3A L-type endospore appendage

EntireName: Recombinant Ena3A L-type endospore appendage
Components
  • Organelle or cellular component: Recombinant Ena3A L-type endospore appendage
    • Protein or peptide: DUF3992 domain-containing protein

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Supramolecule #1: Recombinant Ena3A L-type endospore appendage

SupramoleculeName: Recombinant Ena3A L-type endospore appendage / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus paranthracis (bacteria) / Strain: NVH 0075-95 / Location in cell: spore surface
Molecular weightTheoretical: 18.03 kDa/nm

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Macromolecule #1: DUF3992 domain-containing protein

MacromoleculeName: DUF3992 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Bacillus paranthracis (bacteria)
Molecular weightTheoretical: 11.58715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAQIGNCCTE QLCCVNDAVC CTIILDDTGG TALPIWDDAT TFVINGTIMV ENNGTVGVGP TAALTVNGTA VGGFVVAPGE CRSITMNDI NSIAIVGAGT GTSSVKISFS INYKF

UniProtKB: Endospore appendages core domain-containing protein

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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 / Component - Formula: miliQ
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 8528 / Average electron dose: 62.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 44.97 Å
Applied symmetry - Helical parameters - Δ&Phi: 18.547 °
Applied symmetry - Helical parameters - Axial symmetry: C7 (7 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.3) / Number images used: 454321
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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