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- EMDB-4409: Large subunit of Arabidopsis thaliana mitochondrial ribosome -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-4409
TitleLarge subunit of Arabidopsis thaliana mitochondrial ribosome
Map dataLarge subunit of Arabidopsis thaliana mitochondrial ribosome
Sample
  • Complex: Arabidopsis thaliana mitochondrial ribosome
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsWaltz F / Nguyen T / Arrive M / Bochler A / Chicher J / Hammann P / Kuhn L / Quadrado M / Mireau H / Hashem Y / Giege P
CitationJournal: Nat Plants / Year: 2019
Title: Small is big in Arabidopsis mitochondrial ribosome.
Authors: Florent Waltz / Tan-Trung Nguyen / Mathilde Arrivé / Anthony Bochler / Johana Chicher / Philippe Hammann / Lauriane Kuhn / Martine Quadrado / Hakim Mireau / Yaser Hashem / Philippe Giegé /
Abstract: Mitochondria are responsible for energy production through aerobic respiration, and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like ...Mitochondria are responsible for energy production through aerobic respiration, and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in mitochondrial translation remains unclear. Here we present the biochemical characterization of Arabidopsis mitochondrial ribosomes and identify their protein subunit composition. Complementary biochemical approaches identified 19 plant-specific mitoribosome proteins, of which ten are PPR proteins. The knockout mutations of ribosomal PPR (rPPR) genes result in distinct macroscopic phenotypes, including lethality and severe growth delay. The molecular analysis of rppr1 mutants using ribosome profiling, as well as the analysis of mitochondrial protein levels, demonstrate rPPR1 to be a generic translation factor that is a novel function for PPR proteins. Finally, single-particle cryo-electron microscopy (cryo-EM) reveals the unique structural architecture of Arabidopsis mitoribosomes, characterized by a very large small ribosomal subunit, larger than the large subunit, bearing an additional RNA domain grafted onto the head. Overall, our results show that Arabidopsis mitoribosomes are substantially divergent from bacterial and other eukaryote mitoribosomes, in terms of both structure and protein content.
History
DepositionNov 12, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseJan 23, 2019-
UpdateJan 23, 2019-
Current statusJan 23, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0224
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0224
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4409.png

Downloads & links

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Map

FileDownload / File: emd_4409.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLarge subunit of Arabidopsis thaliana mitochondrial ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 170 pix.
= 374. Å		2.2 Å/pix.
x 170 pix.
= 374. Å		2.2 Å/pix.
x 170 pix.
= 374. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0224 / Movie #1: 0.0224
Minimum - Maximum-0.021896617 - 0.059966736
Average (Standard dev.)0.00094733405 (±0.0081598405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z170170170
origin x/y/z0.0000.0000.000
length x/y/z374.000374.000374.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS170170170
D min/max/mean-0.0220.0600.001

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Supplemental data

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Sample components

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Entire : Arabidopsis thaliana mitochondrial ribosome

EntireName: Arabidopsis thaliana mitochondrial ribosome
Components
  • Complex: Arabidopsis thaliana mitochondrial ribosome

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Supramolecule #1: Arabidopsis thaliana mitochondrial ribosome

SupramoleculeName: Arabidopsis thaliana mitochondrial ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -4.5 µm / Nominal defocus min: -0.6 µm / Nominal magnification: 59000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Number images used: 24000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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