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- EMDB-14097: 3D map of the crystalline organisation of Deinococcus radiodurans... -

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Basic information

Entry
Database: EMDB / ID: EMD-14097
Title3D map of the crystalline organisation of Deinococcus radiodurans' cell envelope
Map data3D map of the crystalline cell wall of Deinococcus radiodurans
Sample
  • Complex: Cell wall's of Deinococcus radiodurans
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Methodelectron crystallography / cryo EM
AuthorsFarci D / Piano D
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science CentrePRO-2017/26/E/NZ1/00344 Poland
Polish National Science CentrePRO-2018/30/M/NZ1/00284 Poland
CitationJournal: 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
DepositionDec 24, 2021-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14097.png

Downloads & links

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Map

FileDownload / File: emd_14097.map.gz / Format: CCP4 / Size: 110.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of the crystalline cell wall of Deinococcus radiodurans
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 200 pix.
= 200. Å		1 Å/pix.
x 380 pix.
= 380. Å		1 Å/pix.
x 380 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 100.0
Minimum - Maximum-648.99567 - 621.4979
Average (Standard dev.)-7.2732603e-10 (±101.4436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-190-1900
Dimensions380380200
Spacing380380200
CellA: 380.0 Å / B: 380.0 Å / C: 200.0 Å
α: 90.0 ° / β: 90.0 ° / γ: 120.0 °

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Supplemental data

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Sample components

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Entire : Cell wall's of Deinococcus radiodurans

EntireName: Cell wall's of Deinococcus radiodurans
Components
  • Complex: Cell wall's of Deinococcus radiodurans

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Supramolecule #1: Cell wall's of Deinococcus radiodurans

SupramoleculeName: Cell wall's of Deinococcus radiodurans / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageTilt 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

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Image processing

Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: FOCUS
Crystal parametersUnit 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 statisticsNumber 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

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