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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of Orrella dioscoreae BcsD | |||||||||
![]() | Sharpened cryo-EM map of Orrella dioscoreae BcsD | |||||||||
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![]() | Bacterial cytoskeleton / bacterial cellulose / bacterial secretion / bacterial biofilms / STRUCTURAL PROTEIN | |||||||||
Function / homology | Cellulose synthase operon protein D, bacterial / Cellulose synthase subunit D superfamily / Cellulose synthase subunit D / cellulose biosynthetic process / Cellulose synthase operon protein D![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.33 Å | |||||||||
![]() | Puygrenier L / Decossas M / Krasteva PV | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() Title: Structures and roles of BcsD and partner scaffold proteins in proteobacterial cellulose secretion. Authors: Thibault G Sana / Areti Notopoulou / Lucie Puygrenier / Marion Decossas / Sandra Moreau / Aurélien Carlier / Petya V Krasteva / ![]() ![]() Abstract: Cellulose is the world's most abundant biopolymer, and similar to its role as a cell wall component in plants, it is a prevalent constituent of the extracellular matrix in bacterial biofilms. ...Cellulose is the world's most abundant biopolymer, and similar to its role as a cell wall component in plants, it is a prevalent constituent of the extracellular matrix in bacterial biofilms. Although bacterial cellulose (BC) was first described in the 19 century, it was only recently revealed that it is produced by several distinct types of Bcs secretion systems that feature multiple accessory subunits in addition to a catalytic BcsAB synthase tandem. We recently showed that crystalline cellulose secretion in the Gluconacetobacter genus (α-Proteobacteria) is driven by a supramolecular BcsH-BcsD scaffold-the "cortical belt"-which stabilizes the synthase nanoarrays through an unexpected inside-out mechanism for secretion system assembly. Interestingly, while bcsH is specific for Gluconacetobacter, bcsD homologs are widespread in Proteobacteria. Here, we examine BcsD homologs and their gene neighborhoods from several plant-colonizing β- and γ-Proteobacteria proposed to secrete a variety of non-crystalline and/or chemically modified cellulosic polymers. We provide structural and mechanistic evidence that through different quaternary structure assemblies BcsD acts with proline-rich BcsH, BcsP, or BcsO partners across the proteobacterial clade to form synthase-interacting intracellular scaffolds that, in turn, determine the biofilm strength and architecture in species with strikingly different physiology and secreted biopolymers. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 96.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.4 KB 21.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 50 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() ![]() ![]() | 48.6 MB 91.3 MB 94.6 MB 94.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 796.4 KB | Display | ![]() |
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Full document | ![]() | 796 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pkdMC ![]() 8pocC ![]() 8pogC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Sharpened cryo-EM map of Orrella dioscoreae BcsD | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.657 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened cryo-EM map of Orrella dioscoreae BcsD
File | emd_17735_additional_1.map | ||||||||||||
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Annotation | Unsharpened cryo-EM map of Orrella dioscoreae BcsD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Deep EMhancer sharpened cryo-EM map of Orrella dioscoreae BcsD
File | emd_17735_additional_2.map | ||||||||||||
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Annotation | Deep EMhancer sharpened cryo-EM map of Orrella dioscoreae BcsD | ||||||||||||
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Density Histograms |
-Half map: EM half-map for O. dioscoreae BcsD
File | emd_17735_half_map_1.map | ||||||||||||
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Annotation | EM half-map for O. dioscoreae BcsD | ||||||||||||
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Density Histograms |
-Half map: EM half-map for O. dioscoreae BcsD
File | emd_17735_half_map_2.map | ||||||||||||
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Annotation | EM half-map for O. dioscoreae BcsD | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Orrella dioscoreae BcsD
Entire | Name: Orrella dioscoreae BcsD |
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Components |
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-Supramolecule #1: Orrella dioscoreae BcsD
Supramolecule | Name: Orrella dioscoreae BcsD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 69.7 KDa |
-Macromolecule #1: Cellulose synthase operon protein D
Macromolecule | Name: Cellulose synthase operon protein D / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 17.448371 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSMENPLFD YYRNRQAPLQ WRGALGALAQ SLTNHFSPEQ LRTLLREAGQ HFASQHPVQA AETVQSMQDA MNGVWTTQDW GWVDIHDLD SFLTLTHYAA PLESAFGAQN LAWSAAFLEG VYEQWFRQLG ASDALHVRQS EESDVRKAIV LRLGR UniProtKB: Cellulose synthase operon protein D |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 16 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 / Details: 100 mM NaCl, 20 mM HEPES pH 8.0 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | The sample was monodispersed, size-exclusion purified protein. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 19118 / Average electron dose: 51.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Details | Iterative model building and refinement in Coot, Namdinator and Phenix. |
Refinement | Space: REAL / Protocol: OTHER |
Output model | ![]() PDB-8pkd: |