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Yorodumi- EMDB-14097: 3D map of the crystalline organisation of Deinococcus radiodurans... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14097 | |||||||||
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Title | 3D map of the crystalline organisation of Deinococcus radiodurans' cell envelope | |||||||||
Map data | 3D map of the crystalline cell wall of Deinococcus radiodurans | |||||||||
Sample |
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Biological species | Deinococcus radiodurans R1 (radioresistant) | |||||||||
Method | electron crystallography / cryo EM | |||||||||
Authors | Farci D / Piano D | |||||||||
Funding support | Poland, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: The structured organization of ' cell envelope. Authors: Domenica Farci / Patrycja Haniewicz / Dario Piano / Abstract: Surface layers (S-layers) are highly ordered coats of proteins localized on the cell surface of many bacterial species. In these structures, one or more proteins form elementary units that self- ...Surface layers (S-layers) are highly ordered coats of proteins localized on the cell surface of many bacterial species. In these structures, one or more proteins form elementary units that self-assemble into a crystalline monolayer tiling the entire cell surface. Here, the cell envelope of the radiation-resistant bacterium was studied by cryo-electron microscopy, finding the crystalline regularity of the S-layer extended into the layers below (outer membrane, periplasm, and inner membrane). The cell envelope appears to be highly packed and resulting from a three-dimensional crystalline distribution of protein complexes organized in close continuity yet allowing a certain degree of free space. The presented results suggest how S-layers, at least in some species, are mesoscale assemblies behaving as structural and functional scaffolds essential for the entire cell envelope. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14097.map.gz | 43.4 MB | EMDB map data format | |
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Header (meta data) | emd-14097-v30.xml emd-14097.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_14097.png | 77.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14097 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14097 | HTTPS FTP |
-Validation report
Summary document | emd_14097_validation.pdf.gz | 518 KB | Display | EMDB validaton report |
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Full document | emd_14097_full_validation.pdf.gz | 517.6 KB | Display | |
Data in XML | emd_14097_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | emd_14097_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14097 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14097 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14097.map.gz / Format: CCP4 / Size: 110.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | 3D map of the crystalline cell wall of Deinococcus radiodurans | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Cell wall's of Deinococcus radiodurans
Entire | Name: Cell wall's of Deinococcus radiodurans |
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Components |
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-Supramolecule #1: Cell wall's of Deinococcus radiodurans
Supramolecule | Name: Cell wall's of Deinococcus radiodurans / type: complex / ID: 1 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Deinococcus radiodurans R1 (radioresistant) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number grids imaged: 40 / Number diffraction images: 73 / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 21000 / Camera length: 800 mm |
Sample stage | Tilt angle: 0.0, 3.0, -3.0, 6.0, -6.0, 9.0, -9.0, 12.0, -12.0, 15.0, -15.0, 18.0, -18.0, 21.0, -21.0, 24.0, -24.0, 27.0, -27.0, 30.0, -30.0, 33.0, -36.0, 39.0, -39.0, 42.0, -42.0, 45.0, -45.0 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: FOCUS |
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Crystal parameters | Unit cell - A: 190 Å / Unit cell - B: 190 Å / Unit cell - C: 200 Å / Unit cell - C sampling length: 200 Å / Unit cell - γ: 120 ° / Plane group: P 6 |
Crystallography statistics | Number intensities measured: 818327 / Number structure factors: 12261 / Fourier space coverage: 95 / R merge: 4.21 / Overall phase residual: 0 Phase error rejection criteria: PHASE ERROR (0/180, 45 is random) High resolution: 4.00293 Å / Shell - Shell ID: 1 / Shell - High resolution: 329.1 Å / Shell - Low resolution: 4.00293 Å / Shell - Number structure factors: 12261 / Shell - Phase residual: 74.731 / Shell - Fourier space coverage: 95 / Shell - Multiplicity: 1 |