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- EMDB-1076: Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA... -

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Basic information

Entry
Database: EMDB / ID: EMD-1076
TitleStructure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
Map dataThis is a volume of 80S ribosome
Sample
  • Sample: the 80S Ribosome from Saccharomyces cerevisiae
  • Complex: 80S ribosome
  • RNA: tRNA
  • Protein or peptide: Sec61
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.4 Å
AuthorsSpahn CM
CitationJournal: Cell / Year: 2001
Title: Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
Authors: C M Spahn / R Beckmann / N Eswar / P A Penczek / A Sali / G Blobel / J Frank /
Abstract: A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and ...A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.
History
DepositionMar 10, 2004-
Header (metadata) releaseApr 7, 2004-
Map releaseApr 7, 2004-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1076.gif

Downloads & links

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Map

FileDownload / File: emd_1076.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a volume of 80S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.93 Å/pix.
x 125 pix.
= 366.25 Å		2.93 Å/pix.
x 125 pix.
= 366.25 Å		2.93 Å/pix.
x 125 pix.
= 366.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.93 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 78.0 / Movie #1: 45
Minimum - Maximum-89.955600000000004 - 227.358000000000004
Average (Standard dev.)4.7599 (±29.0471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-62-62-62
Dimensions125125125
Spacing125125125
CellA=B=C: 366.25 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.932.932.93
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z366.250366.250366.250
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-89.956227.3584.760

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Supplemental data

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Sample components

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Entire : the 80S Ribosome from Saccharomyces cerevisiae

EntireName: the 80S Ribosome from Saccharomyces cerevisiae
Components
  • Sample: the 80S Ribosome from Saccharomyces cerevisiae
  • Complex: 80S ribosome
  • RNA: tRNA
  • Protein or peptide: Sec61

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Supramolecule #1000: the 80S Ribosome from Saccharomyces cerevisiae

SupramoleculeName: the 80S Ribosome from Saccharomyces cerevisiae / type: sample / ID: 1000 / Number unique components: 3
Molecular weightTheoretical: 3.2 MDa

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' yeast

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Macromolecule #1: tRNA

MacromoleculeName: tRNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #2: Sec61

MacromoleculeName: Sec61 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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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

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 93 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 50000
Sample stageSpecimen holder: cryo-transfer / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: defocus group volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

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