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- EMDB-4155: Ribosome-bound membrane insertase YidC -

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Basic information

Entry
Database: EMDB / ID: EMD-4155
TitleRibosome-bound membrane insertase YidC
Map data
Sample
  • Complex: Complex of translationally-stalled ribosome and membrane-embedded YidC insertase
Function / homology
Function and homology information


protein insertion into membrane from inner side / membrane insertase activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / protein insertion into membrane / protein transport / protein folding / protein-containing complex assembly / membrane / plasma membrane
Similarity search - Function
Membrane insertase YidC, N-terminal / YidC, periplasmic domain superfamily / YidC periplasmic domain / Membrane insertase YidC / : / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18
Similarity search - Domain/homology
Membrane protein insertase YidC / Membrane protein insertase YidC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKedrov A / Wickles S / Crevenna AH / van der Sluis EO / Buschauer R / Berninghausen O / Lamb DC / Beckmann R
CitationJournal: Cell Rep / Year: 2016
Title: Structural Dynamics of the YidC:Ribosome Complex during Membrane Protein Biogenesis.
Authors: Alexej Kedrov / Stephan Wickles / Alvaro H Crevenna / Eli O van der Sluis / Robert Buschauer / Otto Berninghausen / Don C Lamb / Roland Beckmann /
Abstract: Members of the YidC/Oxa1/Alb3 family universally facilitate membrane protein biogenesis, via mechanisms that have thus far remained unclear. Here, we investigated two crucial functional aspects: the ...Members of the YidC/Oxa1/Alb3 family universally facilitate membrane protein biogenesis, via mechanisms that have thus far remained unclear. Here, we investigated two crucial functional aspects: the interaction of YidC with ribosome:nascent chain complexes (RNCs) and the structural dynamics of RNC-bound YidC in nanodiscs. We observed that a fully exposed nascent transmembrane domain (TMD) is required for high-affinity YidC:RNC interactions, while weaker binding may already occur at earlier stages of translation. YidC efficiently catalyzed the membrane insertion of nascent TMDs in both fluid and gel phase membranes. Cryo-electron microscopy and fluorescence analysis revealed a conformational change in YidC upon nascent chain insertion: the essential TMDs 2 and 3 of YidC were tilted, while the amphipathic helix EH1 relocated into the hydrophobic core of the membrane. We suggest that EH1 serves as a mechanical lever, facilitating a coordinated movement of YidC TMDs to trigger the release of nascent chains into the membrane.
History
DepositionOct 20, 2016-
Header (metadata) releaseNov 23, 2016-
Map releaseDec 14, 2016-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5m5h
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5m5h
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4155.png

Downloads & links

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Map

FileDownload / File: emd_4155.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 450 pix.
= 487.8 Å		1.08 Å/pix.
x 450 pix.
= 487.8 Å		1.08 Å/pix.
x 450 pix.
= 487.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.040021695 - 0.09104371
Average (Standard dev.)0.0006949382 (±0.005066483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 487.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z487.800487.800487.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.0400.0910.001

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Supplemental data

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Sample components

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Entire : Complex of translationally-stalled ribosome and membrane-embedded...

EntireName: Complex of translationally-stalled ribosome and membrane-embedded YidC insertase
Components
  • Complex: Complex of translationally-stalled ribosome and membrane-embedded YidC insertase

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Supramolecule #1: Complex of translationally-stalled ribosome and membrane-embedded...

SupramoleculeName: Complex of translationally-stalled ribosome and membrane-embedded YidC insertase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pTrc99A

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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: 7.2 / Details: 150 mM KOAc, 5 mM Mg(OAc)2, 25 mM HEPES pH 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 24.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42658
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 10
Final angle assignmentType: PROJECTION MATCHING

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