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

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Basic information

Entry
Database: EMDB / ID: 4155
TitleRibosome-bound membrane insertase YidC
Map data
SampleComplex of translationally-stalled ribosome and membrane-embedded YidC insertase:
Function / homologyMembrane insertase YidC / YidC periplasmic domain / Membrane insertase YidC/ALB3/OXA1/COX18 / Membrane insertase YidC, N-terminal / Membrane insertase YidC/Oxa1, C-terminal / Membrane insertase YidC, periplasmic domain / YidC, periplasmic domain superfamily / 60Kd inner membrane protein / membrane insertase activity / protein insertion into membrane ...Membrane insertase YidC / YidC periplasmic domain / Membrane insertase YidC/ALB3/OXA1/COX18 / Membrane insertase YidC, N-terminal / Membrane insertase YidC/Oxa1, C-terminal / Membrane insertase YidC, periplasmic domain / YidC, periplasmic domain superfamily / 60Kd inner membrane protein / membrane insertase activity / protein insertion into membrane / protein-containing complex assembly / protein folding / protein homooligomerization / integral component of plasma membrane / integral component of membrane / plasma membrane / Membrane protein insertase YidC / Membrane protein insertase YidC
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
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.
Validation ReportPDB-ID: 5m5h

SummaryFull reportAbout validation report
DateDeposition: Oct 20, 2016 / Header (metadata) release: Nov 23, 2016 / Map release: Dec 14, 2016 / Last update: Aug 2, 2017

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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 models: PDB-5m5h
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4155.map.gz (map file in CCP4 format, 364501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
450 pix
1.08 Å/pix.
= 487.8 Å
450 pix
1.08 Å/pix.
= 487.8 Å
450 pix
1.08 Å/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
Contour Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.040021695 - 0.09104371
Average (Standard dev.)0.0006949382 (0.005066483)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions450450450
Origin0.00.00.0
Limit449.0449.0449.0
Spacing450450450
CellA=B=C: 487.8 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
Number of components: 1

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Component #1: protein, Complex of translationally-stalled ribosome and membrane...

ProteinName: Complex of translationally-stalled ribosome and membrane-embedded YidC insertase
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pTrc99A

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 150 mM KOAc, 5 mM Mg(OAc)2, 25 mM HEPES pH 7.2
pH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 24 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 42658
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Output model

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