+Open data
-Basic information
Entry | Database: PDB / ID: 8pkd | ||||||
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Title | Cryo-EM structure of Orrella dioscoreae BcsD | ||||||
Components | Cellulose synthase operon protein D | ||||||
Keywords | STRUCTURAL PROTEIN / Bacterial cytoskeleton / bacterial cellulose / bacterial secretion / bacterial biofilms | ||||||
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 | Orrella dioscoreae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å | ||||||
Authors | Puygrenier, L. / Decossas, M. / Krasteva, P.V. | ||||||
Funding support | European Union, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pkd.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pkd.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 8pkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pkd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8pkd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8pkd_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 8pkd_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/8pkd ftp://data.pdbj.org/pub/pdb/validation_reports/pk/8pkd | HTTPS FTP |
-Related structure data
Related structure data | 17735MC 8pocC 8pogC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 17448.371 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Orrella dioscoreae (bacteria) / Gene: ODI_03820 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C3K6W2 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Orrella dioscoreae BcsD / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.0697 MDa / Experimental value: YES |
Source (natural) | Organism: Orrella dioscoreae (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pRSF-Duet1 |
Buffer solution | pH: 8 / Details: 100 mM NaCl, 20 mM HEPES pH 8.0 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was monodispersed, size-exclusion purified protein. |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 51.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 19118 |
EM imaging optics | Energyfilter name: GIF Quantum LS |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 6563631 | ||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2032604 Details: All refinements (heterorefinement and non-uniform refinement performed in cryoSPARC) Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: Iterative model building and refinement in Coot, Namdinator and Phenix. | ||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |