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- EMDB-15673: Cryo-EM structure of a TasA fibre -

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Basic information

Entry
Database: EMDB / ID: EMD-15673
TitleCryo-EM structure of a TasA fibre
Map dataHelical reconstruction cryo-EM map of TasA fibres.
Sample
  • Complex: Three-subunit TasA filament
    • Protein or peptide: Major biofilm matrix component
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsBoehning J / Bharat TAM
Funding support United Kingdom, 1 items
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 DK / Khalid S / Chai L / Bharat TAM
History
DepositionAug 25, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15673.png

Downloads & links

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Map

FileDownload / File: emd_15673.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction cryo-EM map of TasA fibres.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 280 pix.
= 305.76 Å		1.09 Å/pix.
x 280 pix.
= 305.76 Å		1.09 Å/pix.
x 280 pix.
= 305.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.092 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.048423715 - 0.10818161
Average (Standard dev.)6.771967e-05 (±0.0017658668)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 305.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15673_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15673_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15673_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Three-subunit TasA filament

EntireName: Three-subunit TasA filament
Components
  • Complex: Three-subunit TasA filament
    • Protein or peptide: Major biofilm matrix component

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Supramolecule #1: Three-subunit TasA filament

SupramoleculeName: Three-subunit TasA filament / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: ZK4363
Molecular weightTheoretical: 77.211 KDa

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Macromolecule #1: Major biofilm matrix component

MacromoleculeName: Major biofilm matrix component / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: 168
Molecular weightTheoretical: 25.767654 KDa
SequenceString: AFNDIKSKDA TFASGTLDLS AKENSASVNL SNLKPGDKLT KDFQFENNGS LAIKEVLMAL NYGDFKANGG SNTSPEDFLS QFEVTLLTV GKEGGNGYPK NIILDDANLK DLYLMSAKND AAAAEKIKKQ IDPKFLNASG KVNVATIDGK TAPEYDGVPK T PTDFDQVQ ...String:
AFNDIKSKDA TFASGTLDLS AKENSASVNL SNLKPGDKLT KDFQFENNGS LAIKEVLMAL NYGDFKANGG SNTSPEDFLS QFEVTLLTV GKEGGNGYPK NIILDDANLK DLYLMSAKND AAAAEKIKKQ IDPKFLNASG KVNVATIDGK TAPEYDGVPK T PTDFDQVQ MEIQFKDDKT KDEKGLMVQN KYQGNSIKLQ FSFEATQWNG LTIKKDHTDK DGYVKENEKA HSEDKN

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 48.36 Å
Applied symmetry - Helical parameters - Δ&Phi: -55.18 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 103009
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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