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- EMDB-19559: Human mitochondrial ribosome from elatol treated HEK cells (no tR... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-19559
TitleHuman mitochondrial ribosome from elatol treated HEK cells (no tRNA/mRNA bound)
Map dataLocal resolution filtered,overall masked refined map of the monosome (vacant mRNA channel)
Sample
  • Complex: Human mitoribosome bound to tRNAs/mRNA at partial occupancy
Keywordshuman mitochondria / translation / elatol / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsSingh V / Barrientos A / Amunts A
Funding support Sweden, European Union, 5 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
European Research Council (ERC)European Union
European Molecular Biology Organization (EMBO)European Union
H2020 Marie Curie Actions of the European CommissionEuropean Union
CitationJournal: To Be Published
Title: A Novel Mode of Action Blocking Mitochondrial Translation by the Marine Compound Elatol Promotes Potent Anti-Leukemic Activit
Authors: Nyvltova E / Manara P / Maiti P / Singh V / Cunnigham TA / Amador LA / Rodriguez AD / Wiefels MD / Soste M / Beaton N / Amunts A / Fontanesi F / Schatz JH / Barrientos A
History
DepositionFeb 5, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19559.png

Downloads & links

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Map

FileDownload / File: emd_19559.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered,overall masked refined map of the monosome (vacant mRNA channel)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 540 pix.
= 442.8 Å		0.82 Å/pix.
x 540 pix.
= 442.8 Å		0.82 Å/pix.
x 540 pix.
= 442.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.20885025 - 0.39852923
Average (Standard dev.)0.000062306804 (±0.0069887806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 442.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local resolution filtered map, local masked refined on...

Fileemd_19559_additional_1.map
AnnotationLocal resolution filtered map, local masked refined on SSU-head (vacant mRNA channel)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution filtered map, local masked refined on...

Fileemd_19559_additional_2.map
AnnotationLocal resolution filtered map, local masked refined on SSU-body (vacant mRNA channel)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the monosome (vacant mRNA channel)

Fileemd_19559_half_map_1.map
AnnotationHalf map 2 of the monosome (vacant mRNA channel)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the monosome (vacant mRNA channel)

Fileemd_19559_half_map_2.map
AnnotationHalf map 1 of the monosome (vacant mRNA channel)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human mitoribosome bound to tRNAs/mRNA at partial occupancy

EntireName: Human mitoribosome bound to tRNAs/mRNA at partial occupancy
Components
  • Complex: Human mitoribosome bound to tRNAs/mRNA at partial occupancy

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Supramolecule #1: Human mitoribosome bound to tRNAs/mRNA at partial occupancy

SupramoleculeName: Human mitoribosome bound to tRNAs/mRNA at partial occupancy
type: complex / ID: 1 / Parent: 0 / Details: purified from elatol treated HEK cells
Source (natural)Organism: Homo sapiens (human)

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

13980

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9089
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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