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- EMDB-55568: Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with Se... -

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Basic information

Entry
Database: EMDB / ID: EMD-55568
TitleStructure of a stalled E. coli 70S RNC-NuoK-86 in complex with SecYEG (Consensus Refinement)
Map data
Sample
  • Complex: Stalled E. coli 70S RNC-NuoK-86 in complex with SecYEG-YidC
Keywords70S Ribosome / SecYEG translocon / NuoK / PROTEIN TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsRosales-Hernandez C / Busch M / Kamel M / Kedrov A / Beckmann R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: EMBO J / Year: 2026
Title: Substrate-induced assembly and functional mechanism of the membrane protein insertase SecYEG-YidC.
Authors: Max Busch / Cristian Rosales-Hernandez / Michael Kamel / Yulia Schaumkessel / Eli O van der Sluis / Otto Berninghausen / Thomas Becker / Roland Beckmann / Alexej Kedrov /
Abstract: The Sec translocon and the YidC/Oxa1-type insertases universally mediate biogenesis of α-helical membrane proteins, but the molecular basis of their cooperation has remained disputed. Recent ...The Sec translocon and the YidC/Oxa1-type insertases universally mediate biogenesis of α-helical membrane proteins, but the molecular basis of their cooperation has remained disputed. Recent discovery of multi-subunit insertases assembled at the back of the translocon in fungi and higher eukaryotes has raised questions about the architecture and mechanism of the putative bacterial ortholog SecYEG-YidC. Here, we combine cryogenic electron microscopy with cell-free protein synthesis to visualize biogenesis of the SecYEG/YidC-dependent multipass membrane protein NuoK. The nascent chain of NuoK does not enter the lateral gate of SecYEG but instead crosses the translocon towards its back side, where YidC is recruited in the nascent substrate-dependent manner. The SecY-YidC interface promotes folding of the transmembrane helices before insertion, consistent with thermodynamic principles of membrane protein folding. YidC forms extensive contacts with the nascent chain, suggesting its key role in the insertion event. These findings provide mechanistic insight into membrane protein insertases, support evolutionary conservation of a gate-independent insertion route, and expand current models of membrane protein biogenesis.
History
DepositionNov 4, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55568.png

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 680 pix.
= 494.36 Å		0.73 Å/pix.
x 680 pix.
= 494.36 Å		0.73 Å/pix.
x 680 pix.
= 494.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.680093 - 1.9989251
Average (Standard dev.)0.0011629149 (±0.062582694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 494.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55568_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55568_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 : Stalled E. coli 70S RNC-NuoK-86 in complex with SecYEG-YidC

EntireName: Stalled E. coli 70S RNC-NuoK-86 in complex with SecYEG-YidC
Components
  • Complex: Stalled E. coli 70S RNC-NuoK-86 in complex with SecYEG-YidC

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

SupramoleculeName: Stalled E. coli 70S RNC-NuoK-86 in complex with SecYEG-YidC
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: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 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: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 57156
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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