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- EMDB-51703: High resolution structure of B. oleracea mitoribosome - unfocused -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51703
TitleHigh resolution structure of B. oleracea mitoribosome - unfocused
Map data
Sample
  • Complex: Full flowering plant mitochondrial ribosome
Keywordsmitochondria / mitoribosome / assembly factor / plant / RIBOSOME
Biological speciesBrassica oleracea var. botrytis (cauliflower)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.11 Å
AuthorsWaltz F / Skaltsogiannis V / Giege P
Funding support Germany, Switzerland, 2 items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Swiss National Science Foundation210561 Switzerland
CitationJournal: Nature Communications / Year: 2025
Title: Structural insights into cauliflower mitoribosome in translation state and in association with a late assembly factor
Authors: Skaltsogiannis V / Wolff P / Nguyen T / Corre N / Pflieger D / Blevins T / Hashem Y / Giege P / Waltz F
History
DepositionOct 2, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51703.png

Downloads & links

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Map

FileDownload / File: emd_51703.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 588 pix.
= 551.124 Å		0.94 Å/pix.
x 588 pix.
= 551.124 Å		0.94 Å/pix.
x 588 pix.
= 551.124 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.132
Minimum - Maximum-0.665354 - 1.3016554
Average (Standard dev.)-0.0001468545 (±0.030033786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 551.12396 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51703_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51703_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51703_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full flowering plant mitochondrial ribosome

EntireName: Full flowering plant mitochondrial ribosome
Components
  • Complex: Full flowering plant mitochondrial ribosome

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Supramolecule #1: Full flowering plant mitochondrial ribosome

SupramoleculeName: Full flowering plant mitochondrial ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#37
Source (natural)Organism: Brassica oleracea var. botrytis (cauliflower)

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 41.66 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 343753
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 219403
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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