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- EMDB-13578: C.reinhardtii mitochondrial ribosome (in situ) -

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Basic information

Entry
Database: EMDB / ID: EMD-13578
TitleC.reinhardtii mitochondrial ribosome (in situ)
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 31.6 Å
AuthorsWaltz F / Salinas-Giege T / Englmeier R / Meichel H / Soufari H / Kuhn L / Pfeffer S / Foerster F / Engel BD / Giege P ...Waltz F / Salinas-Giege T / Englmeier R / Meichel H / Soufari H / Kuhn L / Pfeffer S / Foerster F / Engel BD / Giege P / Drouard L / Hashem Y
Funding support Netherlands, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)TransTryp ID:759120 Netherlands
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0057_MITOCROSS Netherlands
Agence Nationale de la Recherche (ANR)MITRA, ANR-16-CE11-0024-02 Netherlands
Agence Nationale de la Recherche (ANR)DAMIA, ANR-20-CE11-0021 Netherlands
Netherlands Organisation for Scientific Research (NWO)Vici 724.016.001 Netherlands
CitationJournal: Nat Commun / Year: 2021
Title: How to build a ribosome from RNA fragments in Chlamydomonas mitochondria.
Authors: Florent Waltz / Thalia Salinas-Giegé / Robert Englmeier / Herrade Meichel / Heddy Soufari / Lauriane Kuhn / Stefan Pfeffer / Friedrich Förster / Benjamin D Engel / Philippe Giegé / ...Authors: Florent Waltz / Thalia Salinas-Giegé / Robert Englmeier / Herrade Meichel / Heddy Soufari / Lauriane Kuhn / Stefan Pfeffer / Friedrich Förster / Benjamin D Engel / Philippe Giegé / Laurence Drouard / Yaser Hashem /
Abstract: Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the ...Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.
History
DepositionSep 10, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.422
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.422
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13578.png

Downloads & links

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Map

FileDownload / File: emd_13578.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.84 Å/pix.
x 96 pix.
= 656.64 Å		6.84 Å/pix.
x 96 pix.
= 656.64 Å		6.84 Å/pix.
x 96 pix.
= 656.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.422 / Movie #1: 0.422
Minimum - Maximum-1.4218955 - 2.1478512
Average (Standard dev.)0.00017554578 (±0.21724841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 656.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z656.640656.640656.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-1.4222.1480.000

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Supplemental data

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Sample components

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Entire : Chlamydomonas reinhardtii

EntireName: Chlamydomonas reinhardtii (plant)
Components
  • Cell: Chlamydomonas reinhardtii

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Supramolecule #1: Chlamydomonas reinhardtii

SupramoleculeName: Chlamydomonas reinhardtii / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 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) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 31.6 Å / Resolution method: FSC 0.33 CUT-OFF / Number subtomograms used: 73
ExtractionNumber tomograms: 27 / Number images used: 222
Final 3D classificationNumber classes: 5 / Avg.num./class: 44
Final angle assignmentType: OTHER

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