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- PDB-7zzy: Solution BcsD structure -

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Basic information

Entry
Database: PDB / ID: 7zzy
TitleSolution BcsD structure
ComponentsCellulose biosynthesis protein
KeywordsSTRUCTURAL PROTEIN / Bacterial cytoskeleton / Crystalline cellulose secretion
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKrasteva, P.V. / Abidi, W. / Decossas, M.
Funding supportEuropean Union, 1items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulose biosynthesis protein
G: Cellulose biosynthesis protein
E: Cellulose biosynthesis protein
C: Cellulose biosynthesis protein
H: Cellulose biosynthesis protein
B: Cellulose biosynthesis protein
D: Cellulose biosynthesis protein
F: Cellulose biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)164,7718
Polymers164,7718
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19050 Å2
ΔGint-126 kcal/mol
Surface area47740 Å2

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Components

#1: Protein
Cellulose biosynthesis protein / Cellulose synthase subunit D


Mass: 20596.332 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: The HRV3c-cleavable hexahistidine tag was cleaved during the purification process. Sample protein sequence starts with PMGSTIFEK...
Source: (gene. exp.) Komagataeibacter hansenii ATCC 23769 (bacteria)
Gene: acsD, GXY_04292 / Plasmid: pProEx-BcsD / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Star DE3 / References: UniProt: Q76KJ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BcsD from G. hansenii / Type: COMPLEX
Details: Octameric BcsD in solution. Expressed recombinantly in E. coli and purified via a cleavable N-terminal hexahistidine tag.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Komagataeibacter hansenii ATCC 23769 (bacteria) / Strain: ATCC 23769
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: Star DE3 / Plasmid: pProEx-Htb
Buffer solutionpH: 8 / Details: 20 mM HEPES pH 8.0, 100 mM NaCl
SpecimenConc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2750 nm / Nominal defocus min: 480 nm / Cs: 2.7 mm
Image recordingElectron dose: 40.59 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
13cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1221383
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 380318 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028928
ELECTRON MICROSCOPYf_angle_d0.46212152
ELECTRON MICROSCOPYf_dihedral_angle_d2.9731192
ELECTRON MICROSCOPYf_chiral_restr0.0361416
ELECTRON MICROSCOPYf_plane_restr0.0041552

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