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- EMDB-8170: Yeast 80S ribosome in the ratcheted state with A/P and P/E tRNAs ... -

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Open data


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Basic information

Entry
Database: EMDB / ID: 8170
TitleYeast 80S ribosome in the ratcheted state with A/P and P/E tRNAs Hel2 bound
Sample80S-Hel2
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataNone
Methodsingle particle reconstruction, at 8.8 A resolution
AuthorsBecker T / Schmidt C
CitationTo be published

To be published Search PubMed
Ubiquitination of Stalled Ribosome Triggers Ribosome-associated Quality Control
Matsuo Y / Ikeuchi K / Saeki Y / Iwasaki S / Schmidt C / Udagawa T / Sato F / Tsuchiya H / Ando K / Becker T / Tanaka K / Ingolia NT / Beckmann R / Inada T

DateDeposition: May 4, 2016 / Header (metadata) release: Jul 6, 2016 / Map release: May 17, 2017 / Last update: May 4, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1300
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 1300
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8170.map.gz (map file in CCP4 format, 202613 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)X (Row.)Y (Col.)
370 pix
1.06 A/pix
= 392.94 A
370 pix
1.06 A/pix
= 392.94 A
370 pix
1.06 A/pix
= 392.94 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.062 A
Density
Contour Level:1300 (by author), 1300 (movie #1):
Minimum - Maximum-4009.6619 - 8260.869
Average (Standard dev.)30.221798 (919.2952)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions370370370
Origin000
Limit369369369
Spacing370370370
CellA=B=C: 392.94 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.0621.0621.062
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z392.940392.940392.940
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ370370370
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-4009.6628260.86930.222

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Supplemental data

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Sample components

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Entire 80S-Hel2

EntireName: 80S-Hel2 / Number of components: 1
MassTheoretical: 4.2 MDa

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Component #1: protein, 80S-Hel2

ProteinName: 80S-Hel2 / Recombinant expression: No
MassTheoretical: 4.2 MDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 27 e/A2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 27172
3D reconstructionSoftware: SPIDER / CTF correction: SPIDER / Resolution: 8.8 A / Resolution method: FSC 0.5 CUT-OFF

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