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- PDB-8pdz: Recombinant Ena3A L-Type endospore appendages -

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Basic information

Entry
Database: PDB / ID: 8pdz
TitleRecombinant Ena3A L-Type endospore appendages
ComponentsDUF3992 domain-containing protein
KeywordsPROTEIN FIBRIL / Endospore / Pili / Protein / Fiber / Spore / Appendage / Bacillus paranthracis / recombinant
Function / homologyEndospore appendages core / Endospore appendages / Endospore appendages core domain-containing protein
Function and homology information
Biological speciesBacillus paranthracis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsSleutel, M. / Remaut, H.
Funding support Belgium, 1items
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, E.D. / Llarena, A.K. / Pradhan, B. / Fislage, M. / O'Sullivan, K. / Aspholm, M. / Remaut, H.
History
DepositionJun 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name
Revision 1.3Sep 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: DUF3992 domain-containing protein
Q: DUF3992 domain-containing protein
P: DUF3992 domain-containing protein
O: DUF3992 domain-containing protein
U: DUF3992 domain-containing protein
T: DUF3992 domain-containing protein
S: DUF3992 domain-containing protein
V: DUF3992 domain-containing protein
W: DUF3992 domain-containing protein
X: DUF3992 domain-containing protein
Y: DUF3992 domain-containing protein
Z: DUF3992 domain-containing protein
a: DUF3992 domain-containing protein
b: DUF3992 domain-containing protein
H: DUF3992 domain-containing protein
I: DUF3992 domain-containing protein
J: DUF3992 domain-containing protein
K: DUF3992 domain-containing protein
L: DUF3992 domain-containing protein
M: DUF3992 domain-containing protein
N: DUF3992 domain-containing protein
A: DUF3992 domain-containing protein
B: DUF3992 domain-containing protein
C: DUF3992 domain-containing protein
D: DUF3992 domain-containing protein
E: DUF3992 domain-containing protein
F: DUF3992 domain-containing protein
G: DUF3992 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)324,44028
Polymers324,44028
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area82270 Å2
ΔGint-594 kcal/mol
Surface area112410 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "P"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_15ens_1chain "O"
d_16ens_1chain "A"
d_17ens_1chain "Q"
d_18ens_1chain "R"
d_19ens_1chain "S"
d_20ens_1chain "T"
d_21ens_1chain "U"
d_22ens_1chain "V"
d_23ens_1chain "W"
d_24ens_1chain "X"
d_25ens_1chain "Y"
d_26ens_1chain "Z"
d_27ens_1chain "a"
d_28ens_1chain "b"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 3 - 115 / Label seq-ID: 2 - 114

Dom-IDAuth asym-IDLabel asym-ID
d_1PC
d_2BW
d_3CX
d_4DY
d_5EZ
d_6FAA
d_7GBA
d_8HO
d_9IP
d_10JQ
d_11KR
d_12LS
d_13MT
d_14NU
d_15OD
d_16AV
d_17QB
d_18RA
d_19SG
d_20TF
d_21UE
d_22VH
d_23WI
d_24XJ
d_25YK
d_26ZL
d_27aM
d_28bN

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Components

#1: Protein ...
DUF3992 domain-containing protein


Mass: 11587.150 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus paranthracis (bacteria)
Gene: AT268_06065, AT274_24635, BKK64_18030, CQZ91_26150, FOC96_02480, FOC96_16350, FOC96_31100, TU58_22910
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J6Z5T8
Has protein modificationY

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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 Ena3A L-type endospore appendage / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 18.03 kDa/nm / Experimental value: NO
Source (natural)Organism: Bacillus paranthracis (bacteria) / Strain: NVH 0075-95 / Cellular location: spore surface
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
Buffer componentFormula: miliQ
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 62.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8528

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Processing

EM software
IDNameVersionCategory
12cryoSPARC4.0.33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 18.547 ° / Axial rise/subunit: 44.97 Å / Axial symmetry: C7
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 454321 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 84.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002122540
ELECTRON MICROSCOPYf_angle_d0.503130828
ELECTRON MICROSCOPYf_chiral_restr0.05123948
ELECTRON MICROSCOPYf_plane_restr0.00434004
ELECTRON MICROSCOPYf_dihedral_angle_d3.73813220
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints2.27071044904E-11
ens_1d_3CELECTRON MICROSCOPYNCS constraints9.92120943738E-13
ens_1d_4CELECTRON MICROSCOPYNCS constraints1.97426590763E-13
ens_1d_5CELECTRON MICROSCOPYNCS constraints3.2192941995E-13
ens_1d_6CELECTRON MICROSCOPYNCS constraints1.16555914407E-13
ens_1d_7CELECTRON MICROSCOPYNCS constraints5.15066555777E-13
ens_1d_8CELECTRON MICROSCOPYNCS constraints6.30944668876E-11
ens_1d_9CELECTRON MICROSCOPYNCS constraints4.1549793163E-12
ens_1d_10CELECTRON MICROSCOPYNCS constraints1.43446089917E-13
ens_1d_11CELECTRON MICROSCOPYNCS constraints2.90491190818E-13
ens_1d_12CELECTRON MICROSCOPYNCS constraints1.90714275876E-13
ens_1d_13CELECTRON MICROSCOPYNCS constraints2.49152679547E-10
ens_1d_14CELECTRON MICROSCOPYNCS constraints2.47372294592E-10
ens_1d_15CELECTRON MICROSCOPYNCS constraints2.62353437819E-13
ens_1d_16CELECTRON MICROSCOPYNCS constraints4.35544805975E-12
ens_1d_17CELECTRON MICROSCOPYNCS constraints4.25117877882E-13
ens_1d_18CELECTRON MICROSCOPYNCS constraints2.90710986354E-13
ens_1d_19CELECTRON MICROSCOPYNCS constraints8.73057371332E-12
ens_1d_20CELECTRON MICROSCOPYNCS constraints2.34831615601E-11
ens_1d_21CELECTRON MICROSCOPYNCS constraints6.73399815904E-12
ens_1d_22CELECTRON MICROSCOPYNCS constraints9.20537627157E-12
ens_1d_23CELECTRON MICROSCOPYNCS constraints2.28406175883E-13
ens_1d_24CELECTRON MICROSCOPYNCS constraints1.97432269653E-10
ens_1d_25CELECTRON MICROSCOPYNCS constraints4.3812138959E-13
ens_1d_26CELECTRON MICROSCOPYNCS constraints9.55712550983E-11
ens_1d_27CELECTRON MICROSCOPYNCS constraints2.4269262436E-13
ens_1d_28CELECTRON MICROSCOPYNCS constraints4.73239762574E-11

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