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- EMDB-6103: Cryo-EM Structure of the 80S-RAC complex from yeast -

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Basic information

Entry
Database: EMDB / ID: EMD-6103
TitleCryo-EM Structure of the 80S-RAC complex from yeast
Map dataReconstruction of yeast 80S-RAC complex, (All particles in Dataset RAC6)
Sample
  • Sample: Saccharomyces cerevisiae 80S ribosome bound with RAC
  • Complex: Saccharomyces cerevisiae 80S ribosome
  • Protein or peptide: Ribosome-associated complex (RAC)
Keywordsribosome-associated complex / co-translational chaperone / cryo-em / translation regulation / Zuotin / Ssz
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.2 Å
AuthorsZhang YX / Ma CY / Yuan Y / Zhu J / Li NN / Chen C / Wu S / Yu L / Lei JL / Gao N
CitationJournal: Nat Struct Mol Biol / Year: 2014
Title: Structural basis for interaction of a cotranslational chaperone with the eukaryotic ribosome.
Authors: Yixiao Zhang / Chengying Ma / Yi Yuan / Jing Zhu / Ningning Li / Chu Chen / Shan Wu / Li Yu / Jianlin Lei / Ning Gao /
Abstract: Cotranslational chaperones, ubiquitous in all living organisms, protect nascent polypeptides from aggregation and facilitate their de novo folding. Importantly, emerging data have also suggested that ...Cotranslational chaperones, ubiquitous in all living organisms, protect nascent polypeptides from aggregation and facilitate their de novo folding. Importantly, emerging data have also suggested that ribosome-associated cotranslational chaperones have active regulatory roles in modulating protein translation. By characterizing the structure of a type of eukaryotic cotranslational chaperone, the ribosome-associated complex (RAC) from Saccharomyces cerevisiae, we show that RAC cross-links two ribosomal subunits, through a single long α-helix, to limit the predominant intersubunit rotation required for peptide elongation. We further demonstrate that any changes in the continuity, length or rigidity of this middle α-helix impair RAC function in vivo. Our results suggest a new mechanism in which RAC directly regulates protein translation by mechanically coupling cotranslational folding with the peptide-elongation cycle, and they lay the foundation for further exploration of regulatory roles of RAC in translation control.
History
DepositionSep 28, 2014-
Header (metadata) releaseOct 22, 2014-
Map releaseOct 22, 2014-
UpdateFeb 24, 2016-
Current statusFeb 24, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.207
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.207
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6103.png

Downloads & links

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Map

FileDownload / File: emd_6103.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of yeast 80S-RAC complex, (All particles in Dataset RAC6)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 168 pix.
= 450.24 Å		2.68 Å/pix.
x 168 pix.
= 450.24 Å		2.68 Å/pix.
x 168 pix.
= 450.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.207 / Movie #1: 0.207
Minimum - Maximum-3.80086064 - 8.607518199999999
Average (Standard dev.)0.0564323 (±0.87305689)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 450.24002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.682.682.68
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z450.240450.240450.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-3.8018.6080.056

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Supplemental data

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Sample components

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Entire : Saccharomyces cerevisiae 80S ribosome bound with RAC

EntireName: Saccharomyces cerevisiae 80S ribosome bound with RAC
Components
  • Sample: Saccharomyces cerevisiae 80S ribosome bound with RAC
  • Complex: Saccharomyces cerevisiae 80S ribosome
  • Protein or peptide: Ribosome-associated complex (RAC)

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Supramolecule #1000: Saccharomyces cerevisiae 80S ribosome bound with RAC

SupramoleculeName: Saccharomyces cerevisiae 80S ribosome bound with RAC / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Saccharomyces cerevisiae 80S ribosome

SupramoleculeName: Saccharomyces cerevisiae 80S ribosome / type: complex / ID: 1 / Recombinant expression: Yes / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Ribosome-associated complex (RAC)

MacromoleculeName: Ribosome-associated complex (RAC) / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: 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: 7.4 / Details: 20 mM Hepes-KOH, 120 mM KOAc, 10 mM Mg(OAc)2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
DateAug 3, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 1721 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles selected by spider. Refinement with spider.
CTF correctionDetails: defocus grouping
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: OTHER / Software - Name: spider / Number images used: 89801
FSC plot (resolution estimation)

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