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- EMDB-1615: Three-dimensional structure of YidC bound to the translating ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-1615
TitleThree-dimensional structure of YidC bound to the translating ribosome
Map dataThis map shows YidC bound to the tunnel exit region of an ribosome nascent chain complex
Sample
  • Sample: YidC bound to a translating ribosome
  • Complex: Ribosome nascent chain complexRibosome-nascent chain complex
  • Protein or peptide: YidC
Keywordsmembrane protein insertion / ribosome / translation
Function / homology: / protein insertion into membrane
Function and homology information
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.4 Å
AuthorsKohler R / Boehringer D / Greber B / Bingel-Erlenmeyer R / Collinson I / Schaffitzel C / Ban N
CitationJournal: Mol Cell / Year: 2009
Title: YidC and Oxa1 form dimeric insertion pores on the translating ribosome.
Authors: Rebecca Kohler / Daniel Boehringer / Basil Greber / Rouven Bingel-Erlenmeyer / Ian Collinson / Christiane Schaffitzel / Nenad Ban /
Abstract: The YidC/Oxa1/Alb3 family of membrane proteins facilitates the insertion and assembly of membrane proteins in bacteria, mitochondria, and chloroplasts. Here we present the structures of both ...The YidC/Oxa1/Alb3 family of membrane proteins facilitates the insertion and assembly of membrane proteins in bacteria, mitochondria, and chloroplasts. Here we present the structures of both Escherichia coli YidC and Saccharomyces cerevisiae Oxa1 bound to E. coli ribosome nascent chain complexes determined by cryo-electron microscopy. Dimers of YidC and Oxa1 are localized above the exit of the ribosomal tunnel. Crosslinking experiments show that the ribosome specifically stabilizes the dimeric state. Functionally important and conserved transmembrane helices of YidC and Oxa1 were localized at the dimer interface by cysteine crosslinking. Both Oxa1 and YidC dimers contact the ribosome at ribosomal protein L23 and conserved rRNA helices 59 and 24, similarly to what was observed for the nonhomologous SecYEG translocon. We suggest that dimers of the YidC and Oxa1 proteins form insertion pores and share a common overall architecture with the SecY monomer.
History
DepositionApr 23, 2009-
Header (metadata) releaseApr 28, 2009-
Map releaseSep 10, 2010-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 40
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 40
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1615_1615.png

Downloads & links

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Map

FileDownload / File: emd_1615.map.gz / Format: CCP4 / Size: 4.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map shows YidC bound to the tunnel exit region of an ribosome nascent chain complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.76 Å/pix.
x 108 pix.
= 406.08 Å		3.76 Å/pix.
x 108 pix.
= 406.08 Å		3.76 Å/pix.
x 108 pix.
= 406.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 40.0 / Movie #1: 40
Minimum - Maximum-191.379999999999995 - 342.406999999999982
Average (Standard dev.)2.54968 (±27.297599999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions108108108
Spacing108108108
CellA=B=C: 406.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.763.763.76
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z406.080406.080406.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS108108108
D min/max/mean-191.380342.4072.550

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Supplemental data

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Sample components

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Entire : YidC bound to a translating ribosome

EntireName: YidC bound to a translating ribosome
Components
  • Sample: YidC bound to a translating ribosome
  • Complex: Ribosome nascent chain complexRibosome-nascent chain complex
  • Protein or peptide: YidC

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Supramolecule #1000: YidC bound to a translating ribosome

SupramoleculeName: YidC bound to a translating ribosome / type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 2.6 MDa / Theoretical: 2.6 MDa

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Supramolecule #1: Ribosome nascent chain complex

SupramoleculeName: Ribosome nascent chain complex / type: complex / ID: 1 / Name.synonym: Translating ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightExperimental: 2.6 MDa / Theoretical: 2.6 MDa

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Macromolecule #1: YidC

MacromoleculeName: YidC / type: protein_or_peptide / ID: 1 / Name.synonym: Membrane protein insertase / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Location in cell: Membrane
Molecular weightExperimental: 62 KDa / Theoretical: 62 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: peT24a
SequenceGO: protein insertion into membrane / InterPro: INTERPRO: IPR013308

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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

GridDetails: 200 mesh copper
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunger

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Average electron dose: 15 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Each image
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.4 Å / Resolution method: OTHER / Software - Name: Imagic-5 Spider / Number images used: 24395

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