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- EMDB-4408: Small subunit of Arabidopsis thaliana mitochondrial ribosome -

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Basic information

Entry
Database: EMDB / ID: 4408
TitleSmall subunit of Arabidopsis thaliana mitochondrial ribosome
Map dataMitochondrial ribosome small subunit from Arabidopsis thaliana
SampleArabidopsis thaliana mitochondrial ribosome:
SourceArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / 21 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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0186
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0186
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4408.map.gz (map file in CCP4 format, 87809 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
280 pix
2.2 Å/pix.
= 616. Å
280 pix
2.2 Å/pix.
= 616. Å
280 pix
2.2 Å/pix.
= 616. 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
Contour Level:0.0186 (by author), 0.0186 (movie #1):
Minimum - Maximum-0.026543515 - 0.08244341
Average (Standard dev.)-0.00004541137 (0.004309513)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions280280280
Origin0.00.00.0
Limit279.0279.0279.0
Spacing280280280
CellA=B=C: 616.0 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/z280280280
origin x/y/z0.0000.0000.000
length x/y/z616.000616.000616.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0270.082-0.000

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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 / Number of components: 1

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Component #1: protein, Arabidopsis thaliana mitochondrial ribosome

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

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Experimental details

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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 %

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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)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 19000
3D reconstructionResolution: 21 Å / Resolution method: OTHER

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