+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15039 | |||||||||
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Title | BcsH-BcsD 'beads-on-a-string' filament, local refine | |||||||||
Map data | BcsHD 'beads-on-a-string' filaments : Unsharpened locally refined map of a BcsH-bound dimer of BcsD octamers | |||||||||
Sample |
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Keywords | Bacterial cytoskeleton / cellulose secretion / STRUCTURAL PROTEIN | |||||||||
Function / homology | Cellulose-complementing protein / Cellulose-complementing protein A / Cellulose synthase operon protein D, bacterial / Cellulose synthase subunit D superfamily / Cellulose synthase subunit D / cellulose biosynthetic process / Cellulose-complementing protein / Cellulose biosynthesis protein Function and homology information | |||||||||
Biological species | Komagataeibacter hansenii ATCC 23769 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Krasteva PV / Abidi W / Decossas M | |||||||||
Funding support | European Union, France, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15039.map.gz | 174.5 MB | EMDB map data format | |
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Header (meta data) | emd-15039-v30.xml emd-15039.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15039_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_15039.png | 94 KB | ||
Masks | emd_15039_msk_1.map | 347.6 MB | Mask map | |
Filedesc metadata | emd-15039.cif.gz | 6.5 KB | ||
Others | emd_15039_additional_1.map.gz emd_15039_half_map_1.map.gz emd_15039_half_map_2.map.gz | 328.2 MB 323.1 MB 323.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15039 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15039 | HTTPS FTP |
-Validation report
Summary document | emd_15039_validation.pdf.gz | 858.3 KB | Display | EMDB validaton report |
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Full document | emd_15039_full_validation.pdf.gz | 857.9 KB | Display | |
Data in XML | emd_15039_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | emd_15039_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15039 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15039 | HTTPS FTP |
-Related structure data
Related structure data | 7zzqMC 7zzyC 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_15039.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | BcsHD 'beads-on-a-string' filaments : Unsharpened locally refined map of a BcsH-bound dimer of BcsD octamers | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.839 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15039_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: BcsHD 'beads-on-a-string' filaments : Autosharpened locally refined map...
File | emd_15039_additional_1.map | ||||||||||||
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Annotation | BcsHD 'beads-on-a-string' filaments : Autosharpened locally refined map of a BcsH-bound dimer of BcsD octamers | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15039_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: BcsHD 'beads-on-a-string' filaments : half map B
File | emd_15039_half_map_2.map | ||||||||||||
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Annotation | BcsHD 'beads-on-a-string' filaments : half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BcsHD 'beads-on-a-string' cis-filaments
Entire | Name: BcsHD 'beads-on-a-string' cis-filaments |
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Components |
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-Supramolecule #1: BcsHD 'beads-on-a-string' cis-filaments
Supramolecule | Name: BcsHD 'beads-on-a-string' cis-filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: G. hansenii BcsHD complex purified after the co-expression of hexahistidine tagged BcsH C-terminal domain and full-length BcsD. IMAC purification via BcsH, tag and linker removed during purification |
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Source (natural) | Organism: Komagataeibacter hansenii ATCC 23769 (bacteria) / Strain: ATCC 23769 |
-Macromolecule #1: Cellulose biosynthesis protein
Macromolecule | Name: Cellulose biosynthesis protein / type: protein_or_peptide / ID: 1 Details: BcsD from Gluconacetobacter hansenii ATCC 23769 expressed recombinantly in BL21 Star DE3 cells Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Komagataeibacter hansenii ATCC 23769 (bacteria) |
Molecular weight | Theoretical: 17.532963 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MGSTIFEKKP DFTLFLQTLS WEIDDQVGIE VRNELLREVG RGMGTRIMPP PCQTVDKLQI ELNALLALIG WGTVTLELLS EDQSLRIVH ENLPQVGSAG EPSGTWLAPV LEGLYGRWVT SQAGAFGDYV VTRDVDAEDL NAVPRQTIIM YMRVRSSAT UniProtKB: Cellulose biosynthesis protein |
-Macromolecule #2: BcsH fragment
Macromolecule | Name: BcsH fragment / type: protein_or_peptide / ID: 2 Details: BcsH C-terminal domain from G. hansenii expressed from a pProEx-Htb vector with a HRV3c-cleavable hexahistidine tag Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Komagataeibacter hansenii ATCC 23769 (bacteria) |
Molecular weight | Theoretical: 9.919921 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MSYYHHHHHH DYDIPTTLEV LFQGPMGSTK TDTNSSQASR PGSPVASPDG SPTMAEVFMT LGGRATELLS PRPSLREALL RRRENEEES UniProtKB: Cellulose-complementing protein |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 105 / 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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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Details: 20 mM NaCl, 100 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: 293 K / Instrument: FEI VITROBOT MARK IV |
Details | Filaments of various sizes eluting in the void volume of a Superdex 200 Increase size-exclusion column. |
-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 BIOQUANTUM (6k x 4k) / Average electron dose: 49.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Model building with Coot, refinement with Phenix and Namdinator |
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
Output model | PDB-7zzq: |