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- EMDB-14095: Subtomogram average of Deinococcus radiodurans' cell envelope -

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Basic information

Entry
Database: EMDB / ID: EMD-14095
TitleSubtomogram average of Deinococcus radiodurans' cell envelope
Map dataSubtomogram average of Deinococcus radiodurans' cell wall
Sample
  • Complex: Cell wall's of Deinococcus radiodurans
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Methodsubtomogram averaging / cryo EM / Resolution: 50.0 Å
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_14095.png

Downloads & links

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Map

FileDownload / File: emd_14095.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of Deinococcus radiodurans' cell wall
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.28 Å/pix.
x 200 pix.
= 456. Å		2.28 Å/pix.
x 200 pix.
= 456. Å		2.28 Å/pix.
x 200 pix.
= 456. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-6466.3623 - 3776.847
Average (Standard dev.)-2353.825 (±815.4449)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 456.0 Å
α=β=γ: 90.0 °

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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
Processingsubtomogram averaging
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) / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 68000
ExtractionNumber tomograms: 40 / Number images used: 4000
Final angle assignmentType: MAXIMUM LIKELIHOOD
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

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