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- EMDB-15041: Solution BcsD structure -

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Basic information

Entry
Database: EMDB / ID: EMD-15041
TitleSolution BcsD structure
Map dataBcsD octamer in solution : Unsharpened cryo-EM map
Sample
  • Complex: BcsD from G. hansenii
    • Protein or peptide: Cellulose biosynthesis protein
  • Ligand: water
KeywordsBacterial cytoskeleton / Crystalline cellulose secretion / STRUCTURAL PROTEIN
Function / homologyCellulose synthase operon protein D, bacterial / Cellulose synthase subunit D superfamily / Cellulose synthase subunit D / cellulose biosynthetic process / Cellulose biosynthesis protein
Function and homology information
Biological speciesKomagataeibacter hansenii ATCC 23769 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15041.png

Downloads & links

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Map

FileDownload / File: emd_15041.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBcsD octamer in solution : Unsharpened cryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.098923765 - 0.43423778
Average (Standard dev.)-0.0003106045 (±0.013091735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15041_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: BcsD octamer in solution : Autosharpened cryo-EM map (cryoSPARC)

Fileemd_15041_additional_1.map
AnnotationBcsD octamer in solution : Autosharpened cryo-EM map (cryoSPARC)
Projections & Slices
AxesZYX

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Half map: BcsD octamer in solution : half map A

Fileemd_15041_half_map_1.map
AnnotationBcsD octamer in solution : half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: BcsD octamer in solution : half map B

Fileemd_15041_half_map_2.map
AnnotationBcsD octamer in solution : half map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : BcsD from G. hansenii

EntireName: BcsD from G. hansenii
Components
  • Complex: BcsD from G. hansenii
    • Protein or peptide: Cellulose biosynthesis protein
  • Ligand: water

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Supramolecule #1: BcsD from G. hansenii

SupramoleculeName: BcsD from G. hansenii / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Octameric BcsD in solution. Expressed recombinantly in E. coli and purified via a cleavable N-terminal hexahistidine tag.
Source (natural)Organism: Komagataeibacter hansenii ATCC 23769 (bacteria) / Strain: ATCC 23769

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Macromolecule #1: Cellulose biosynthesis protein

MacromoleculeName: Cellulose biosynthesis protein / type: protein_or_peptide / ID: 1
Details: The HRV3c-cleavable hexahistidine tag was cleaved during the purification process. Sample protein sequence starts with PMGSTIFEK...
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Komagataeibacter hansenii ATCC 23769 (bacteria)
Molecular weightTheoretical: 20.596332 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSYYHHHHHH DYDIPTTLEV LFQGPMGSTI FEKKPDFTLF LQTLSWEIDD QVGIEVRNEL LREVGRGMGT RIMPPPCQTV DKLQIELNA LLALIGWGTV TLELLSEDQS LRIVHENLPQ VGSAGEPSGT WLAPVLEGLY GRWVTSQAGA FGDYVVTRDV D AEDLNAVP RQTIIMYMRV RSSAT

UniProtKB: Cellulose biosynthesis protein

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 8 / Details: 20 mM HEPES pH 8.0, 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.59 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 0.48 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1221383
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3a8e

Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 380318
Initial angle assignmentType: OTHER / Details: cryoSPARC Ab initio model generation
Final angle assignmentType: OTHER / Details: cryoSPARC Ab initio model generation
FSC plot (resolution estimation)

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