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- EMDB-50012: Structure of the flowering plant mitoribosome with P-site tRNA, l... -

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Basic information

Entry
Database: EMDB / ID: EMD-50012
TitleStructure of the flowering plant mitoribosome with P-site tRNA, large subunit focused
Map data
Sample
  • Complex: Flowering plant mitochondrial ribosome in presence of P-site tRNA
KeywordsMitochondria / tRNA / mitoribosome / ribosome / plant
Biological speciesBrassica oleracea var. botrytis (cauliflower)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWaltz F / Skaltsogiannis V
Funding support Germany, Switzerland, 2 items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Swiss National Science Foundation210561 Switzerland
CitationJournal: To Be Published
Title: Structure of the flowering plant mitoribosome with P-site tRNA, large subunit focused
Authors: Waltz F / Skaltsogiannis V
History
DepositionApr 2, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50012.png

Downloads & links

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Map

FileDownload / File: emd_50012.map.gz / Format: CCP4 / Size: 684.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 564 pix.
= 596.712 Å		1.06 Å/pix.
x 564 pix.
= 596.712 Å		1.06 Å/pix.
x 564 pix.
= 596.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0782
Minimum - Maximum-0.2592243 - 0.55783963
Average (Standard dev.)-0.00030295033 (±0.019142926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions564564564
Spacing564564564
CellA=B=C: 596.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50012_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50012_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50012_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 : Flowering plant mitochondrial ribosome in presence of P-site tRNA

EntireName: Flowering plant mitochondrial ribosome in presence of P-site tRNA
Components
  • Complex: Flowering plant mitochondrial ribosome in presence of P-site tRNA

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Supramolecule #1: Flowering plant mitochondrial ribosome in presence of P-site tRNA

SupramoleculeName: Flowering plant mitochondrial ribosome in presence of P-site tRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#88
Source (natural)Organism: Brassica oleracea var. botrytis (cauliflower) / Organ: Flower / 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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 45.0 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: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34964
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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