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- PDB-8aur: Cryo-EM structure of a TasA fibre -

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Basic information

Entry
Database: PDB / ID: 8aur
TitleCryo-EM structure of a TasA fibre
ComponentsMajor biofilm matrix component
KeywordsPROTEIN FIBRIL / Biofilm matrix fibre
Function / homologyPeptidase M73, camelysin / Camelysin metallo-endopeptidase / Signal peptide, camelysin / sporulation resulting in formation of a cellular spore / extracellular region / identical protein binding / Major biofilm matrix component
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsBoehning, J. / Bharat, T.A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust202231/Z/16/Z United Kingdom
Citation
Journal: Nat Commun / Year: 2022
Title: Donor-strand exchange drives assembly of the TasA scaffold in Bacillus subtilis biofilms.
Authors: Jan Böhning / Mnar Ghrayeb / Conrado Pedebos / Daniel K Abbas / Syma Khalid / Liraz Chai / Tanmay A M Bharat /
Abstract: Many bacteria in nature exist in multicellular communities termed biofilms, where cells are embedded in an extracellular matrix that provides rigidity to the biofilm and protects cells from chemical ...Many bacteria in nature exist in multicellular communities termed biofilms, where cells are embedded in an extracellular matrix that provides rigidity to the biofilm and protects cells from chemical and mechanical stresses. In the Gram-positive model bacterium Bacillus subtilis, TasA is the major protein component of the biofilm matrix, where it has been reported to form functional amyloid fibres contributing to biofilm structure and stability. Here, we present electron cryomicroscopy structures of TasA fibres, which show that, rather than forming amyloid fibrils, TasA monomers assemble into fibres through donor-strand exchange, with each subunit donating a β-strand to complete the fold of the next subunit along the fibre. Combining electron cryotomography, atomic force microscopy, and mutational studies, we show how TasA fibres congregate in three dimensions to form abundant fibre bundles that are essential for B. subtilis biofilm formation. Our study explains the previously observed biochemical properties of TasA and shows how a bacterial extracellular globular protein can assemble from monomers into β-sheet-rich fibres, and how such fibres assemble into bundles in biofilms.
#1: Journal: Biorxiv / Year: 2022
Title: Molecular architecture of the TasA biofilm scaffold in Bacillus subtilis
Authors: Bohning, J. / Ghrayeb, M. / Pedebos, C. / Abbas, D.K. / Khalid, S. / Chai, L. / Bharat, T.A.M.
History
DepositionAug 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major biofilm matrix component
B: Major biofilm matrix component
C: Major biofilm matrix component


Theoretical massNumber of molelcules
Total (without water)77,3033
Polymers77,3033
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7930 Å2
ΔGint-27 kcal/mol
Surface area34550 Å2
MethodPISA

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Components

#1: Protein Major biofilm matrix component / Spore coat-associated protein N / Translocation-dependent antimicrobial spore component


Mass: 25767.654 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / Strain: 168 / References: UniProt: P54507

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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: Three-subunit TasA filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.077211 MDa / Experimental value: NO
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: ZK4363
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
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 / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION3.1CTF correction
12RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -55.18 ° / Axial rise/subunit: 48.36 Å / Axial symmetry: C1
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103009 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025493
ELECTRON MICROSCOPYf_angle_d0.4817386
ELECTRON MICROSCOPYf_dihedral_angle_d3.838714
ELECTRON MICROSCOPYf_chiral_restr0.038807
ELECTRON MICROSCOPYf_plane_restr0.002978

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