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

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Basic information

Database: EMDB / ID: 4409
TitleLarge subunit of Arabidopsis thaliana mitochondrial ribosome
Map dataLarge subunit of Arabidopsis thaliana mitochondrial ribosome
SampleArabidopsis thaliana mitochondrial ribosome:
SourceArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / 16 Å resolution
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
DateDeposition: Nov 12, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019

Structure visualization

  • 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
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_4409.map.gz (map file in CCP4 format, 19653 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
170 pix
2.2 Å/pix.
= 374. Å
170 pix
2.2 Å/pix.
= 374. Å
170 pix
2.2 Å/pix.
= 374. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Contour Level:0.0224 (by author), 0.0224 (movie #1):
Minimum - Maximum-0.021896617 - 0.059966736
Average (Standard dev.)0.00094733405 (0.0081598405)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 374.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0220.0600.001

Supplemental data

Sample components

Entire Arabidopsis thaliana mitochondrial ribosome

EntireName: Arabidopsis thaliana mitochondrial ribosome / Number of components: 1

Component #1: protein, Arabidopsis thaliana mitochondrial ribosome

ProteinName: Arabidopsis thaliana mitochondrial ribosome / Recombinant expression: No
SourceSpecies: Arabidopsis thaliana (thale cress)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: -600.0 - -4500.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 24000
3D reconstructionResolution: 16 Å / Resolution method: OTHER

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