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- EMDB-14588: Cryo-EM map of the Xenopus egg dormant ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-14588
TitleCryo-EM map of the Xenopus egg dormant ribosome
Map data
Sample
  • Complex: Xenopus egg 80S ribosome
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLeesch F / Lorenzo-Orts L / Grishkovskaya I / Belacic K / Kandolf S / Lin T-Y / Meinhart A / Haselbach D / Pauli A
Funding support Austria, Switzerland, 5 items
OrganizationGrant numberCountry
Austrian Research Promotion AgencyFFG-852936 Austria
Austrian Science FundSTART Projekt Y 1031-B28 Austria
Austrian Science FundSFB RNA-Deco F 80 Austria
Swiss National Science FoundationP2GEP3_191204 Switzerland
European Molecular Biology Organization (EMBO)ALTF 1165-2019
CitationJournal: Nature / Year: 2023
Title: A molecular network of conserved factors keeps ribosomes dormant in the egg.
Authors: Friederike Leesch / Laura Lorenzo-Orts / Carina Pribitzer / Irina Grishkovskaya / Josef Roehsner / Anastasia Chugunova / Manuel Matzinger / Elisabeth Roitinger / Katarina Belačić / Susanne ...Authors: Friederike Leesch / Laura Lorenzo-Orts / Carina Pribitzer / Irina Grishkovskaya / Josef Roehsner / Anastasia Chugunova / Manuel Matzinger / Elisabeth Roitinger / Katarina Belačić / Susanne Kandolf / Tzi-Yang Lin / Karl Mechtler / Anton Meinhart / David Haselbach / Andrea Pauli /
Abstract: Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed. Here, using mass spectrometry and cryo-electron ...Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4-eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.
History
DepositionMar 24, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14588.png

Downloads & links

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Map

FileDownload / File: emd_14588.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-3.107867 - 6.4136314
Average (Standard dev.)-0.0013680963 (±0.2479025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_14588_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14588_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Xenopus egg 80S ribosome

EntireName: Xenopus egg 80S ribosome
Components
  • Complex: Xenopus egg 80S ribosome

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Supramolecule #1: Xenopus egg 80S ribosome

SupramoleculeName: Xenopus egg 80S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#81
Source (natural)Organism: Xenopus laevis (African clawed frog) / Tissue: Egg

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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: 7.6
Component:
ConcentrationFormulaName
5.0 mMMg(OAc)2Magnesium acetate
20.0 mMHEPES
100.0 mMKClpotassium cholride
1.0 mMDTTDithiotreitol
10.0 mMNH4Clammonium cholride
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.14)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.14)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 86482

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