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- EMDB-13481: Small subunit of the Chlamydomonas mitoribosome - head focus -

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Basic information

Entry
Database: EMDB / ID: EMD-13481
TitleSmall subunit of the Chlamydomonas mitoribosome - head focus
Map dataSmall subunit of the Chlamydomonas mitoribosome - head focus
Sample
  • Complex: Small subunit of the Chlamydomonas mitoribosome - head focus
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.47 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 France, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)TransTryp ID:759120 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0057_MITOCROSS France
Agence Nationale de la Recherche (ANR)MITRA, ANR-16-CE11-0024-02 France
Agence Nationale de la Recherche (ANR)DAMIA, ANR-20-CE11-0021 France
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
DepositionAug 27, 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: 0.0175
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13481.png

Downloads & links

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Map

FileDownload / File: emd_13481.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSmall subunit of the Chlamydomonas mitoribosome - head focus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 360 pix.
= 406.8 Å		1.13 Å/pix.
x 360 pix.
= 406.8 Å		1.13 Å/pix.
x 360 pix.
= 406.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0175 / Movie #1: 0.0175
Minimum - Maximum-0.03492756 - 0.07545682
Average (Standard dev.)0.00015480196 (±0.0029242674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 406.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z406.800406.800406.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0350.0750.000

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Supplemental data

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Sample components

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Entire : Small subunit of the Chlamydomonas mitoribosome - head focus

EntireName: Small subunit of the Chlamydomonas mitoribosome - head focus
Components
  • Complex: Small subunit of the Chlamydomonas mitoribosome - head focus

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Supramolecule #1: Small subunit of the Chlamydomonas mitoribosome - head focus

SupramoleculeName: Small subunit of the Chlamydomonas mitoribosome - head focus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#54
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: Mitochondria

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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

Concentration1.5 mg/mL
BufferpH: 7.6
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 40131
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 6 / Software - Name: RELION

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