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- EMDB-53584: Structure of a stalled E. coli 70S RNC-NuoK-86-E36K-E76K-mutant i... -

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Basic information

Entry
Database: EMDB / ID: EMD-53584
TitleStructure of a stalled E. coli 70S RNC-NuoK-86-E36K-E76K-mutant in complex with the SecYEG-YidC membrane protein insertase
Map data
Sample
  • Complex: E. coli 70S RNC-NuoK-86-mut in complex with the SecYEG-YidC membrane protein insertase
Keywords70S Ribosome / SecYEG translocon / YidC / NuoK / PROTEIN TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsRosales-Hernandez C / Busch M / Kamel M / Beckmann R / Kedrov A
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Substrate-induced assembly of the SecYEG-YidC membrane protein insertase
Authors: Busch M / Rosales-Hernandez C / Kamel M / Schaumkessel Y / van der Sluis E / Berninghausen O / Becker T / Beckmann R / Kedrov A
History
DepositionMay 8, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53584.png

Downloads & links

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Map

FileDownload / File: emd_53584.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 480 pix.
= 503.52 Å		1.05 Å/pix.
x 480 pix.
= 503.52 Å		1.05 Å/pix.
x 480 pix.
= 503.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.049 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.34125924 - 2.5319169
Average (Standard dev.)0.024149423 (±0.15168858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 503.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53584_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53584_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 : E. coli 70S RNC-NuoK-86-mut in complex with the SecYEG-YidC membr...

EntireName: E. coli 70S RNC-NuoK-86-mut in complex with the SecYEG-YidC membrane protein insertase
Components
  • Complex: E. coli 70S RNC-NuoK-86-mut in complex with the SecYEG-YidC membrane protein insertase

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Supramolecule #1: E. coli 70S RNC-NuoK-86-mut in complex with the SecYEG-YidC membr...

SupramoleculeName: E. coli 70S RNC-NuoK-86-mut in complex with the SecYEG-YidC membrane protein insertase
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48952
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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