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- PDB-9h3d: F-ENA exosporium anchoring complex between ExsF and a peptide der... -

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Basic information

Entry
Database: PDB / ID: 9h3d
TitleF-ENA exosporium anchoring complex between ExsF and a peptide derived from the N-terminus of F-Anchor
Components
  • DUF4183 domain-containing protein
  • Exosporium protein ExsF
KeywordsSTRUCTURAL PROTEIN / Endospore appendage / ENA / Bacillus / fiber / ExsF / BclA / F-ENA
Function / homologyDomain of unknown function DUF4183 / Domain of unknown function (DUF4183) / : / Leader peptide, exosporium / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / DUF4183 domain-containing protein / :
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSogues, A. / Sleutel, M. / Remaut, H.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 709-2021European Union
H2020 Marie Curie Actions of the European CommissionSLYDIVEuropean Union
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
DepositionOct 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF4183 domain-containing protein
B: DUF4183 domain-containing protein
C: DUF4183 domain-containing protein
D: Exosporium protein ExsF
E: Exosporium protein ExsF
F: Exosporium protein ExsF
G: DUF4183 domain-containing protein
H: DUF4183 domain-containing protein
I: DUF4183 domain-containing protein
J: Exosporium protein ExsF
K: Exosporium protein ExsF
L: Exosporium protein ExsF


Theoretical massNumber of molelcules
Total (without water)110,38812
Polymers110,38812
Non-polymers00
Water13,349741
1
A: DUF4183 domain-containing protein
B: DUF4183 domain-containing protein
C: DUF4183 domain-containing protein
D: Exosporium protein ExsF
E: Exosporium protein ExsF
F: Exosporium protein ExsF


Theoretical massNumber of molelcules
Total (without water)55,1946
Polymers55,1946
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-63 kcal/mol
Surface area15170 Å2
MethodPISA
2
G: DUF4183 domain-containing protein
H: DUF4183 domain-containing protein
I: DUF4183 domain-containing protein
J: Exosporium protein ExsF
K: Exosporium protein ExsF
L: Exosporium protein ExsF


Theoretical massNumber of molelcules
Total (without water)55,1946
Polymers55,1946
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-57 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.292, 91.809, 99.931
Angle α, β, γ (deg.)90.000, 101.567, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein/peptide
DUF4183 domain-containing protein


Mass: 2226.523 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Bacillus thuringiensis (bacteria) / References: UniProt: A0A643M7W3
#2: Protein
Exosporium protein ExsF


Mass: 16171.468 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: exsF, REY75_14105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAP5G885
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 6% w/v PEG3350, 0.15 M Sodium Chloride and 4M Potassium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.92→50.25 Å / Num. obs: 69027 / % possible obs: 100 % / Redundancy: 6 % / Rpim(I) all: 0.103 / Net I/σ(I): 5.9
Reflection shellResolution: 1.92→10 Å / Num. unique obs: 3362 / Rpim(I) all: 0.969

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→50.25 Å / SU ML: 0.2281 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 3363 4.93 %
Rwork0.1843 64912 -
obs0.1859 68275 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.61 Å2
Refinement stepCycle: LAST / Resolution: 1.92→50.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7144 0 0 741 7885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00697301
X-RAY DIFFRACTIONf_angle_d0.847110058
X-RAY DIFFRACTIONf_chiral_restr0.06291267
X-RAY DIFFRACTIONf_plane_restr0.00771318
X-RAY DIFFRACTIONf_dihedral_angle_d13.81812597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.37021080.33892380X-RAY DIFFRACTION86.6
1.95-1.980.3261310.31162455X-RAY DIFFRACTION90.51
1.98-2.010.30741370.29372613X-RAY DIFFRACTION97.21
2.01-2.040.30481670.28192704X-RAY DIFFRACTION99.38
2.04-2.080.33711380.27082707X-RAY DIFFRACTION99.55
2.08-2.110.29031430.25442741X-RAY DIFFRACTION99.72
2.11-2.160.28591590.24242719X-RAY DIFFRACTION99.9
2.16-2.20.25481480.24842683X-RAY DIFFRACTION99.93
2.2-2.250.28391310.24222766X-RAY DIFFRACTION99.83
2.25-2.30.2921250.21742741X-RAY DIFFRACTION99.72
2.3-2.360.27241320.21652704X-RAY DIFFRACTION99.93
2.36-2.420.23551330.22122769X-RAY DIFFRACTION99.86
2.42-2.490.28271520.21432700X-RAY DIFFRACTION99.82
2.49-2.570.23651470.2012733X-RAY DIFFRACTION99.93
2.57-2.660.27211320.19162729X-RAY DIFFRACTION99.9
2.66-2.770.21281350.17652738X-RAY DIFFRACTION99.97
2.77-2.90.21081110.17762746X-RAY DIFFRACTION99.83
2.9-3.050.19691390.17942753X-RAY DIFFRACTION99.93
3.05-3.240.22341600.17722728X-RAY DIFFRACTION99.93
3.24-3.490.19791590.1552724X-RAY DIFFRACTION99.97
3.49-3.840.20521420.15432742X-RAY DIFFRACTION99.93
3.84-4.40.14631390.12892761X-RAY DIFFRACTION100
4.4-5.540.14031560.11912757X-RAY DIFFRACTION99.93
5.54-50.250.14461390.15082819X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: 22.1329569815 Å / Origin y: 0.508446408105 Å / Origin z: 60.6588811399 Å
111213212223313233
T0.195833808037 Å20.000942166900476 Å2-0.0360174415537 Å2-0.0880285727865 Å20.00621162954854 Å2--0.134257739871 Å2
L0.177716669252 °2-0.00431924062053 °20.0507373772038 °2-0.890604485197 °20.0316388347109 °2--0.475279558849 °2
S0.0132784969874 Å °-0.0278619726708 Å °-0.0254926104663 Å °0.340232021639 Å °0.0210955328939 Å °-0.08093182975 Å °0.0290317995784 Å °0.036067015057 Å °-0.0115766493453 Å °
Refinement TLS groupSelection details: all

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