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- EMDB-10605: Map of the 80S Mouse ribosome with A- and P-site tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-10605
TitleMap of the 80S Mouse ribosome with A- and P-site tRNA
Map dataMap of the 80S Mouse ribosome with A- and P-site tRNA
Sample
  • Complex: Mouse 80S ribosome in complex with A and P-site tRNA and EBP1
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKraushar M / Krupp F / Sprink T / Buerger J / Mielke T / Spahn CMT
Funding support Germany, United States, 4 items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
German Research Foundation (DFG)25065445 Germany
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)5F30MH106220-02 United States
European Molecular Biology Organization (EMBO)190-2016 Germany
CitationJournal: Mol.Cell / Year: 2021
Title: Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.
Authors: Kraushar ML / Krupp F / Harnett D / Turko P / Ambrozkiewicz MC / Sprink T / Imami K / Gunnigmann M / Zinnall U / Vieira-Vieira CH / Schaub T / Munster-Wandowski A / Burger J / Borisova E / ...Authors: Kraushar ML / Krupp F / Harnett D / Turko P / Ambrozkiewicz MC / Sprink T / Imami K / Gunnigmann M / Zinnall U / Vieira-Vieira CH / Schaub T / Munster-Wandowski A / Burger J / Borisova E / Yamamoto H / Rasin MR / Ohler U / Beule D / Mielke T / Tarabykin V / Landthaler M / Kramer G / Vida I / Selbach M / Spahn CMT
History
DepositionJan 13, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10605.png

Downloads & links

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Map

FileDownload / File: emd_10605.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the 80S Mouse ribosome with A- and P-site tRNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 360 pix.
= 477.36 Å		1.33 Å/pix.
x 360 pix.
= 477.36 Å		1.33 Å/pix.
x 360 pix.
= 477.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.326 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-9.96759 - 20.455547
Average (Standard dev.)0.0009417106 (±0.8934559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 477.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3261.3261.326
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z477.360477.360477.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-9.96820.4560.001

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Supplemental data

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Sample components

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Entire : Mouse 80S ribosome in complex with A and P-site tRNA and EBP1

EntireName: Mouse 80S ribosome in complex with A and P-site tRNA and EBP1
Components
  • Complex: Mouse 80S ribosome in complex with A and P-site tRNA and EBP1

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Supramolecule #1: Mouse 80S ribosome in complex with A and P-site tRNA and EBP1

SupramoleculeName: Mouse 80S ribosome in complex with A and P-site tRNA and EBP1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 31.78 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 14973
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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