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- EMDB-2705: A structural model of the active ribosome-bound membrane protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-2705
TitleA structural model of the active ribosome-bound membrane protein insertase YidC
Map dataCryo-em reconstruction of YidC bound a ribosome nascent chain complex
Sample
  • Sample: Monomeric YidC bound to ribosome nascent chain complex(F0c)
  • Complex: Ribosome nascent chain complex
  • Protein or peptide: YidC
Keywordsribosome / YidC / protein translocation / bioinformatics / MD simulation / membrane
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 / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex / protein insertion into membrane / proton motive force-driven ATP synthesis / : / proton-transporting ATPase activity, rotational mechanism ...protein insertion into membrane from inner side / membrane insertase activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex / protein insertion into membrane / proton motive force-driven ATP synthesis / : / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / protein folding / protein-containing complex assembly / lipid binding / 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 / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C ...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 / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
Membrane protein insertase YidC / ATP synthase subunit c
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsWickles S / Singharoy A / Andreani J / Seemayer S / Bischoff L / Berninghausen O / Soeding J / Schulten K / van der Sluis EO / Beckmann R
CitationJournal: Elife / Year: 2014
Title: A structural model of the active ribosome-bound membrane protein insertase YidC.
Authors: Stephan Wickles / Abhishek Singharoy / Jessica Andreani / Stefan Seemayer / Lukas Bischoff / Otto Berninghausen / Johannes Soeding / Klaus Schulten / Eli O van der Sluis / Roland Beckmann /
Abstract: The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a ...The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.
History
DepositionJul 10, 2014-
Header (metadata) releaseJul 23, 2014-
Map releaseJul 23, 2014-
UpdateAug 27, 2014-
Current statusAug 27, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4utq
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4utq
  • Surface level: 0.35
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4utq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2705.png

Downloads & links

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Map

FileDownload / File: emd_2705.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-em reconstruction of YidC bound a ribosome nascent chain complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 368 pix.
= 380.88 Å		1.04 Å/pix.
x 368 pix.
= 380.88 Å		1.04 Å/pix.
x 368 pix.
= 380.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.035 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.25 / Movie #1: 0.35
Minimum - Maximum-0.53752744 - 1.26601863
Average (Standard dev.)0.00298494 (±0.13338423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 380.87997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0351.0351.035
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z380.880380.880380.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-0.5381.2660.003

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Supplemental data

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Sample components

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Entire : Monomeric YidC bound to ribosome nascent chain complex(F0c)

EntireName: Monomeric YidC bound to ribosome nascent chain complex(F0c)
Components
  • Sample: Monomeric YidC bound to ribosome nascent chain complex(F0c)
  • Complex: Ribosome nascent chain complex
  • Protein or peptide: YidC

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Supramolecule #1000: Monomeric YidC bound to ribosome nascent chain complex(F0c)

SupramoleculeName: Monomeric YidC bound to ribosome nascent chain complex(F0c)
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Ribosome nascent chain complex

SupramoleculeName: Ribosome nascent chain complex / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: YidC

MacromoleculeName: YidC / type: protein_or_peptide / ID: 1 / Recombinant expression: No
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

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJun 1, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 9999 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.3 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Defocus group
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 58960

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