9H38 | pdb_00009h38

C-terminal domain of the F-ENA tip fibrillum F-BclA from Bacillus thuringiensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Cryo-EM analysis of the Bacillus thuringiensis extrasporal matrix identifies F-ENA as a widespread family of endospore appendages across the Firmicutes phylum.

Sleutel, M.Sogues, A.Gerven, N.V.Jonsmoen, U.L.Molle, I.V.Fislage, M.Theunissen, L.D.Bellis, N.F.Baquero, D.P.Egelman, E.H.Krupovic, M.Wang, F.Aspholm, M.Remaut, H.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.02.11.637640
  • Primary Citation Related Structures: 
    9H38, 9H3D, 9I0Y

  • PubMed 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 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 Bacillus, Anaerovorax and Paenibaccilus 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 Bacillus , 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.


  • Organizational Affiliation
    • Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.

Macromolecule Content 

  • Total Structure Weight: 323.43 kDa 
  • Atom Count: 22,780 
  • Modeled Residue Count: 2,898 
  • Deposited Residue Count: 3,108 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Flagellar hook-length control protein FliK
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U
148Bacillus thuringiensisMutation(s): 0 
Gene Names: BK775_04930
UniProt
Find proteins for A0A9X6QBI1 (Bacillus thuringiensis)
Explore A0A9X6QBI1 
Go to UniProtKB:  A0A9X6QBI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9X6QBI1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth G],
BA [auth H],
CA [auth J],
V [auth A],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
DA [auth N],
X [auth D],
Y [auth E],
Z [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.826α = 60.11
b = 113.486β = 89.19
c = 113.599γ = 86.36
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European UnionALTF 709-2021
H2020 Marie Curie Actions of the European CommissionEuropean UnionSLYDIV

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release