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- PDB-9hze: CryoEM structure of F-ENA fibers on the spores of Bacillus thurin... -

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Basic information

Entry
Database: PDB / ID: 9hze
TitleCryoEM structure of F-ENA fibers on the spores of Bacillus thuringiensis serovar kurstaki
ComponentsDUF4183 domain-containing protein
KeywordsPROTEIN FIBRIL / ENA / endospore appendage / protein fiber / helical
Function / homology:
Function and homology information
Biological speciesBacillus thuringiensis serovar kurstaki (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsSleutel, M. / Remaut, H.
Funding support Belgium, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DUF4183 domain-containing protein
D: DUF4183 domain-containing protein
E: DUF4183 domain-containing protein
F: DUF4183 domain-containing protein
G: DUF4183 domain-containing protein
H: DUF4183 domain-containing protein
I: DUF4183 domain-containing protein
J: DUF4183 domain-containing protein
K: DUF4183 domain-containing protein
L: DUF4183 domain-containing protein
M: DUF4183 domain-containing protein
N: DUF4183 domain-containing protein
O: DUF4183 domain-containing protein
P: DUF4183 domain-containing protein
Q: DUF4183 domain-containing protein
R: DUF4183 domain-containing protein
S: DUF4183 domain-containing protein
T: DUF4183 domain-containing protein
U: DUF4183 domain-containing protein
V: DUF4183 domain-containing protein
W: DUF4183 domain-containing protein
X: DUF4183 domain-containing protein
Y: DUF4183 domain-containing protein
Z: DUF4183 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)232,63024
Polymers232,63024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
DUF4183 domain-containing protein


Mass: 9692.923 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki (bacteria)
Gene: HW133_20635
Production host: Bacillus thuringiensis serovar kurstaki (bacteria)
References: UniProt: A0AAX0C6N4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: F-ENA / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 8.627 kDa/nm / Experimental value: NO
Source (natural)Organism: Bacillus thuringiensis serovar kurstaki (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEM4.1image acquisition
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 42.73 ° / Axial rise/subunit: 33.54 Å / Axial symmetry: C3
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196540 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL

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