+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17788 | |||||||||
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Title | Cryo-EM structure of Dickeya dadantii BcsD | |||||||||
Map data | Sharpened cryo-EM map for Dickeya dadantii BcsD | |||||||||
Sample |
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Keywords | Cellulose secretion / bacterial biofilms / cytoskeleton / CYTOSOLIC 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 Function and homology information | |||||||||
Biological species | Dickeya dadantii 3937 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Notopoulou A / Krasteva PV | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Curr Biol / Year: 2024 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 | emd_17788.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-17788-v30.xml emd-17788.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
Images | emd_17788.png | 106.3 KB | ||
Masks | emd_17788_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-17788.cif.gz | 6 KB | ||
Others | emd_17788_additional_1.map.gz emd_17788_additional_2.map.gz emd_17788_half_map_1.map.gz emd_17788_half_map_2.map.gz | 30.9 MB 56.6 MB 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17788 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17788 | HTTPS FTP |
-Validation report
Summary document | emd_17788_validation.pdf.gz | 793.2 KB | Display | EMDB validaton report |
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Full document | emd_17788_full_validation.pdf.gz | 792.8 KB | Display | |
Data in XML | emd_17788_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_17788_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17788 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17788 | HTTPS FTP |
-Related structure data
Related structure data | 8pocMC 8pkdC 8pogC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17788.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened cryo-EM map for Dickeya dadantii BcsD | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17788_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened experimental cryo-EM map for Dickeya dadantii BcsD
File | emd_17788_additional_1.map | ||||||||||||
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Annotation | Unsharpened experimental cryo-EM map for Dickeya dadantii BcsD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Deep EMhancer sharpened cryo-EM map for Dickeya dadantii BcsD
File | emd_17788_additional_2.map | ||||||||||||
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Annotation | Deep EMhancer sharpened cryo-EM map for Dickeya dadantii BcsD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map for Dickeya dadantii BcsD
File | emd_17788_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM half map for Dickeya dadantii BcsD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map for Dickeya dadantii BcsD
File | emd_17788_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM half map for Dickeya dadantii BcsD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tetrameric BcsD of Dickeya dadantii
Entire | Name: Tetrameric BcsD of Dickeya dadantii |
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Components |
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-Supramolecule #1: Tetrameric BcsD of Dickeya dadantii
Supramolecule | Name: Tetrameric BcsD of Dickeya dadantii / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Dickeya dadantii 3937 (bacteria) |
Molecular weight | Theoretical: 70 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: Dickeya dadantii 3937 (bacteria) |
Molecular weight | Theoretical: 17.930289 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSMSDLQQH ALNYYRQQQL PSGWADLFGV IVNGMMDNAG EREGLAFLRH IGGQLAERYP LPAAVTVVDL EREINRVLSL FHWGCVDLR PYENRLEIYH LALPASVNSS GSVRWRMAMA AVLQGLYSRW LREQGGVESV PLSCEETDSE STLLFRYQH UniProtKB: Cellulose synthase operon protein D |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 / Details: 20 mM HEPES pH 8.0, 120 mM NaCl |
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 |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 0-50 / Average electron dose: 52.9 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Details | Reiterative refinement in Phenix, Coot and Namdinator |
Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-8poc: |