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- EMDB-10606: Map of the 80S Mouse ribosome with eEF2. -

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Basic information

Entry
Database: EMDB / ID: EMD-10606
TitleMap of the 80S Mouse ribosome with eEF2.
Map dataMap of the 80S Mouse ribosome with eEF2
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: 3.1 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: Matthew L Kraushar / Ferdinand Krupp / Dermot Harnett / Paul Turko / Mateusz C Ambrozkiewicz / Thiemo Sprink / Koshi Imami / Manuel Günnigmann / Ulrike Zinnall / Carlos H Vieira-Vieira / ...Authors: Matthew L Kraushar / Ferdinand Krupp / Dermot Harnett / Paul Turko / Mateusz C Ambrozkiewicz / Thiemo Sprink / Koshi Imami / Manuel Günnigmann / Ulrike Zinnall / Carlos H Vieira-Vieira / Theres Schaub / Agnieszka Münster-Wandowski / Jörg Bürger / Ekaterina Borisova / Hiroshi Yamamoto / Mladen-Roko Rasin / Uwe Ohler / Dieter Beule / Thorsten Mielke / Victor Tarabykin / Markus Landthaler / Günter Kramer / Imre Vida / Matthias Selbach / Christian M T Spahn /
Abstract: Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during ...Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during neurogenesis, revealing Ebp1 as a high-occupancy 60S peptide tunnel exit (TE) factor during protein synthesis at near-atomic resolution by cryoelectron microscopy (cryo-EM). Ribosome profiling demonstrated Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regulating ribosome occupancy of these codons. Membrane-targeting domains emerging from the 60S tunnel, which recruit SRP/Sec61 to the shared binding site, displace Ebp1. Ebp1 is particularly abundant in the early-born neural stem cell (NSC) lineage and regulates neuronal morphology. Ebp1 especially impacts the synthesis of membrane-targeted cell adhesion molecules (CAMs), measured by pulsed stable isotope labeling by amino acids in cell culture (pSILAC)/bioorthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry (MS). Therefore, Ebp1 is a central component of protein synthesis, and the ribosome TE is a focal point of gene expression control in the molecular specification of neuronal morphology during development.
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_10606.png

Downloads & links

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Map

FileDownload / File: emd_10606.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the 80S Mouse ribosome with eEF2
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-10.158482 - 18.409008
Average (Standard dev.)-0.00021714455 (±0.9918302)
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-10.15818.409-0.000

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 29466
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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