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- EMDB-16562: Structure of the yeast delta uL16m mitochondrial ribosome assembl... -

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Basic information

Entry
Database: EMDB / ID: EMD-16562
TitleStructure of the yeast delta uL16m mitochondrial ribosome assembly intermediate - State 1
Map dataState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, consensus map
Sample
  • Complex: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m
KeywordsYeast mitochondrial ribosome / delta uL16 / RIBOSOME
Biological speciesSaccharomyces cerevisiae W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsConrad J / Rathore S / Barrientos A
Funding support United States, Sweden, Germany, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118141 United States
Swedish Research Council201803694 Sweden
Knut and Alice Wallenberg Foundation2017009 Sweden
German Research Foundation (DFG)SFB860 Germany
CitationJournal: To Be Published
Title: The late stages of yeast mitoribosome large subunit biogenesis
Authors: Rathore S / Conrad J / De Silva D / Ferrari A / Bouquio D / Kim H-J / Urlaub H / Ott M / Barrientos A
History
DepositionJan 27, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16562.png

Downloads & links

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Map

FileDownload / File: emd_16562.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.09 Å/pix.
x 360 pix.
= 392.4 Å		1.09 Å/pix.
x 360 pix.
= 392.4 Å		1.09 Å/pix.
x 360 pix.
= 392.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.2
Minimum - Maximum-11.15354 - 19.629411999999999
Average (Standard dev.)-0.000000000005267 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 392.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large...

Fileemd_16562_additional_1.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, LSU body
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large subunit, CP

Fileemd_16562_additional_2.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, CP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: State 1, delta uL16m, yeast mitochondrial ribosome, large...

Fileemd_16562_additional_3.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, E-site tRNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State 1, delta uL16m, yeast mitochondrial ribosome, large...

Fileemd_16562_half_map_1.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State 1, delta uL16m, yeast mitochondrial ribosome, large...

Fileemd_16562_half_map_2.map
AnnotationState 1, delta uL16m, yeast mitochondrial ribosome, large subunit, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Large subunit of the yeast mitochondrial ribosome- State 1, delta...

EntireName: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m
Components
  • Complex: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m

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Supramolecule #1: Large subunit of the yeast mitochondrial ribosome- State 1, delta...

SupramoleculeName: Large subunit of the yeast mitochondrial ribosome- State 1, delta uL16m
type: complex / ID: 1 / Parent: 0
Details: Mitoribosomal particles from an uL16m-deletion strain were purified by sucrose cushion sedimentation of mitochondrial extracts prepared in the presence of 20% Mg2+ and 1% Triton X-100. This ...Details: Mitoribosomal particles from an uL16m-deletion strain were purified by sucrose cushion sedimentation of mitochondrial extracts prepared in the presence of 20% Mg2+ and 1% Triton X-100. This approach revealed the structures of novel mitoribosome assembly intermediates. After processing, the structural characterization of the uL16m-deletion mitoribosome particles allowed us to define two major states: state 1, state 2.
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: delta uL16m / 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

BufferpH: 7.4
GridModel: EMS Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 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: EMDB MAP
EMDB ID:

3551

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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