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- EMDB-100010: In situ structure of the 100S disome from Geobacter metallireducens -

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Basic information

Entry
Database: EMDB / ID: EMD-100010
TitleIn situ structure of the 100S disome from Geobacter metallireducens
Map data
Sample
  • Cell: Geobacter metallireducens GS-15
Keywordsdisome 100S Geobacter metallireducens anaerobic metabolism subtomogram averaging in situ cryo-electron tomography ribosome / RIBOSOME
Biological speciesGeobacter metallireducens GS-15 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 8.8 Å
AuthorsTamborrini D / Pascoa TC / Engel BD / Appel L / Kumar A / Kayastha K / Ermler U / Kettler T / Bohn S / Reif-Trauttmansdorff T ...Tamborrini D / Pascoa TC / Engel BD / Appel L / Kumar A / Kayastha K / Ermler U / Kettler T / Bohn S / Reif-Trauttmansdorff T / Schuller JM / Boll M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)European Union
CitationJournal: To Be Published
Title: Coupling of electron-bifurcation modules powers aromatic ring reduction
Authors: Appel L / Kumar A / Tamborrini D / Pascoa TC / Kayastha K / Ermler U / Kettler T / Bohn S / Reif-Trauttmansdorff T / Engel BD / Schuller JM / Boll M
History
DepositionSep 21, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_100010.png

Downloads & links

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Map

FileDownload / File: emd_100010.map.gz / Format: CCP4 / Size: 357 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.91 Å/pix.
x 454 pix.
= 867.14 Å		1.91 Å/pix.
x 454 pix.
= 867.14 Å		1.91 Å/pix.
x 454 pix.
= 867.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.8
Minimum - Maximum0.0 - 12.991816
Average (Standard dev.)0.046530798 (±0.5082677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions454454454
Spacing454454454
CellA=B=C: 867.14 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_100010_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_100010_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_100010_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Geobacter metallireducens GS-15

EntireName: Geobacter metallireducens GS-15 (bacteria)
Components
  • Cell: Geobacter metallireducens GS-15

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Supramolecule #1: Geobacter metallireducens GS-15

SupramoleculeName: Geobacter metallireducens GS-15 / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Geobacter metallireducens GS-15 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsEER files
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 2.0.0)
Details: Final reconstructions and half-maps were generated with Mcore (Warp 2.0.0)
Number subtomograms used: 2057
ExtractionNumber tomograms: 32 / Number images used: 2057 / Method: NN-distance / Software - Name: Warp (ver. 2.0.0)
Details: 4114 disome-forming ribosomes selected by NN-distance <30A. Recentered at the dimerization contact point
CTF correctionSoftware - Name: Warp (ver. 2.0.0)
Software - details: WarpTools fs_motion_and_ctf & WarpTools ts_ctf & MCore
Details: WarpTools fs_motion_and_ctf WarpTools ts_ctf MCore / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 1 / Avg.num./class: 2057 / Software - Name: RELION (ver. 4.0.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Software:
Namedetails
RELION (ver. 4.0.2)
Warp (ver. 2.0.0)MCore
FSC plot (resolution estimation)

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