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- EMDB-15040: BcsHD cis-filaments: four 'beads-on-a-string' -

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Basic information

Entry
Database: EMDB / ID: EMD-15040
TitleBcsHD cis-filaments: four 'beads-on-a-string'
Map dataBcsHD 'beads-on-a-string' filaments : Unsharpened locally refined map of a BcsH-bound tetramer of BcsD octamers
Sample
  • Complex: BcsHD 'beads-on-a-string' cis-filaments
    • Other: BcsHD 'beads-on-a-string' cis-filaments
Biological speciesKomagataeibacter hansenii ATCC 23769 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsKrasteva PV / Abidi W / Decossas M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)BioMatrix-ERC-2017-StGEuropean Union
CitationJournal: Sci Adv / Year: 2022
Title: Bacterial crystalline cellulose secretion via a supramolecular BcsHD scaffold.
Authors: Wiem Abidi / Marion Decossas / Lucía Torres-Sánchez / Lucie Puygrenier / Sylvie Létoffé / Jean-Marc Ghigo / Petya V Krasteva /
Abstract: Cellulose, the most abundant biopolymer on Earth, is not only the predominant constituent of plants but also a key extracellular polysaccharide in the biofilms of many bacterial species. Depending on ...Cellulose, the most abundant biopolymer on Earth, is not only the predominant constituent of plants but also a key extracellular polysaccharide in the biofilms of many bacterial species. Depending on the producers, chemical modifications, and three-dimensional assemblies, bacterial cellulose (BC) can present diverse degrees of crystallinity. Highly ordered, or crystalline, cellulose presents great economical relevance due to its ever-growing number of biotechnological applications. Even if some acetic acid bacteria have long been identified as BC superproducers, the molecular mechanisms determining the secretion of crystalline versus amorphous cellulose remain largely unknown. Here, we present structural and mechanistic insights into the role of the accessory subunits BcsH (CcpAx) and BcsD (CesD) that determine crystalline BC secretion in the lineage. We show that oligomeric BcsH drives the assembly of BcsD into a supramolecular cytoskeletal scaffold that likely stabilizes the cellulose-extruding synthase nanoarrays through an unexpected inside-out mechanism for secretion system assembly.
History
DepositionMay 26, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15040.png

Downloads & links

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Map

FileDownload / File: emd_15040.map.gz / Format: CCP4 / Size: 548.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBcsHD 'beads-on-a-string' filaments : Unsharpened locally refined map of a BcsH-bound tetramer of BcsD octamers
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 524 pix.
= 553.74 Å		1.06 Å/pix.
x 524 pix.
= 553.74 Å		1.06 Å/pix.
x 524 pix.
= 553.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05676 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.36844268 - 1.4439992
Average (Standard dev.)-0.000949411 (±0.028483221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions524524524
Spacing524524524
CellA=B=C: 553.74 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15040_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: BcsHD 'beads-on-a-string' filaments :Autosharpened locally refined map of...

Fileemd_15040_additional_1.map
AnnotationBcsHD 'beads-on-a-string' filaments :Autosharpened locally refined map of a BcsH-bound tetramer of BcsD octamers
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BcsHD 'beads-on-a-string' filaments : half-map B

Fileemd_15040_half_map_1.map
AnnotationBcsHD 'beads-on-a-string' filaments : half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BcsHD 'beads-on-a-string' filaments : half-map A

Fileemd_15040_half_map_2.map
AnnotationBcsHD 'beads-on-a-string' filaments : half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BcsHD 'beads-on-a-string' cis-filaments

EntireName: BcsHD 'beads-on-a-string' cis-filaments
Components
  • Complex: BcsHD 'beads-on-a-string' cis-filaments
    • Other: BcsHD 'beads-on-a-string' cis-filaments

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Supramolecule #1: BcsHD 'beads-on-a-string' cis-filaments

SupramoleculeName: BcsHD 'beads-on-a-string' cis-filaments / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: BcsHD filaments purified upon coexpression of BcsD (no tag) and BcsH C-terminal region carrying an HRV3c-cleavable N-terminal hexahistidine tag.
Source (natural)Organism: Komagataeibacter hansenii ATCC 23769 (bacteria) / Strain: ATCC 23769 / Location in cell: cytoskeleton

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Macromolecule #1: BcsHD 'beads-on-a-string' cis-filaments

MacromoleculeName: BcsHD 'beads-on-a-string' cis-filaments / type: other / ID: 1
Details: Multiple copies of BcsD and BcsH (protein in sample is tag-free with sequence: PMGSTKTDTNSSQASRPGSPVASPDGSPTMAEVFMTLGGRATELLSPRPSLREALLRRRENEEES) in BcsH-driven cis-filaments
Classification: other
Source (natural)Organism: Komagataeibacter hansenii ATCC 23769 (bacteria) / Strain: ATCC 23769
SequenceString:
BcsD MGSTK TDTNSSQASR PGSPVASPDG SPTMAEVFMT LGGRATELLS PRPSLREALL RRRENEEES BcsH MSYYH HHHHHDYDIP TTLEVLFQGP MGSTKTDTNS SQASRPGSPV ASPDGSPTMA EVFMTLGGRA TELLSPRPSL REALLRRREN EEES
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Details: 20 mM HEPES pH 8.0, 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber temperature: 20 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.75 µm / Nominal defocus min: 0.48 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2849271
Details: 2849271 auto-picked in cryosparc; 1305940 in final model
Startup modelType of model: OTHER / Details: Ab initio (cryosparc)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 1305940
Initial angle assignmentType: OTHER / Details: Ab-initio model generation in cryoSPARC
Final angle assignmentType: OTHER / Details: Ab-initio model generation in cryoSPARC
FSC plot (resolution estimation)

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