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- PDB-9i65: Recombinant F-ENA-2 fibers -

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Basic information

Entry
Database: PDB / ID: 9i65
TitleRecombinant F-ENA-2 fibers
ComponentsDUF4183 domain-containing protein
KeywordsPROTEIN FIBRIL / endospore appendage / ENA / helical / protein fiber / bacillus thuringiensis serovar kurstaki
Function / homologyDomain of unknown function DUF4183 / Domain of unknown function (DUF4183) / membrane / DUF4183 domain-containing protein
Function and homology information
Biological speciesCohnella sp. OV330 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 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 29, 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
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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

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)120,8109
Polymers120,8109
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: 13423.285 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cohnella sp. OV330 (bacteria) / Gene: SAMN05216312_11547 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I1C8X4
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: Recombinant F-ENA-2 fibers / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Cohnella sp. OV330 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 67.5 ° / Axial rise/subunit: 95.25 Å / Axial symmetry: C3
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286873 / Symmetry type: HELICAL
RefinementHighest resolution: 4.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038595
ELECTRON MICROSCOPYf_angle_d0.60311889
ELECTRON MICROSCOPYf_dihedral_angle_d4.891260
ELECTRON MICROSCOPYf_chiral_restr0.0471593
ELECTRON MICROSCOPYf_plane_restr0.0051503

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