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- EMDB-52430: Mouse mitoribosome large subunit assembly intermediate bound to N... -

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Basic information

Entry
Database: EMDB / ID: EMD-52430
TitleMouse mitoribosome large subunit assembly intermediate bound to NSUN4, MTERF4 and the MALSU1-L0R8F8-mtACP complex, State C2 (SAMC knock-out)
Map data
Sample
  • Complex: Mouse mitochondrial large subunit intermediate
KeywordsMitochondria / ribosome / large subunit / assembly
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsSingh V / Glasgow R / Rorbach J / Freyer C / Amunts A / Wredenberg A
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: The mitochondrial methylation potential gates mitoribosome assembly
Authors: Glasgow R / Singh V / Pena-Perez L / Wilhalm A / Moedas MF / Moore D / Rosenberger FA / Xinping L / Atanassov I / Saba M / Cipullo M / Rorbach J / Wedell A / Freyer C / Amunts A / Wredenberg A
History
DepositionDec 25, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52430.png

Downloads & links

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Map

FileDownload / File: emd_52430.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 540 pix.
= 456.84 Å		0.85 Å/pix.
x 540 pix.
= 456.84 Å		0.85 Å/pix.
x 540 pix.
= 456.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.846 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.014804827 - 0.043012116
Average (Standard dev.)-0.000121744204 (±0.0012393605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 456.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52430_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_52430_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 : Mouse mitochondrial large subunit intermediate

EntireName: Mouse mitochondrial large subunit intermediate
Components
  • Complex: Mouse mitochondrial large subunit intermediate

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Supramolecule #1: Mouse mitochondrial large subunit intermediate

SupramoleculeName: Mouse mitochondrial large subunit intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77377
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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