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- EMDB-65424: Human mitoribosome isolated from 1mM neomycin treated cells, clas... -

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Basic information

Entry
Database: EMDB / ID: EMD-65424
TitleHuman mitoribosome isolated from 1mM neomycin treated cells, class partially rotated state with A/P-site and P/E-site tRNAs
Map data
Sample
  • Complex: Human mitoribosome isolated from 1mM neomycin treated cells, class partially rotated state with A/P-site and P/E-site tRNAs
Keywordsmitoribosome / neomycin / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhu L / Jia C / Wu M / Li W
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171291 China
National Natural Science Foundation of China (NSFC)32371351 China
CitationJournal: To Be Published
Title: Human ribosome interactions reframe neomycin toxicity
Authors: Zhang X / Zhu L / Jia C / Wu K / Bai Y / Sun S / Zhang Z / Guo L / Hou X / Wu M / Amunts A / Li W
History
DepositionJul 19, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65424.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 680 pix.
= 552.16 Å		0.81 Å/pix.
x 680 pix.
= 552.16 Å		0.81 Å/pix.
x 680 pix.
= 552.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.812 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.7372814 - 2.6317225
Average (Standard dev.)-0.0017413943 (±0.08297369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 552.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65424_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_65424_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 : Human mitoribosome isolated from 1mM neomycin treated cells, clas...

EntireName: Human mitoribosome isolated from 1mM neomycin treated cells, class partially rotated state with A/P-site and P/E-site tRNAs
Components
  • Complex: Human mitoribosome isolated from 1mM neomycin treated cells, class partially rotated state with A/P-site and P/E-site tRNAs

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Supramolecule #1: Human mitoribosome isolated from 1mM neomycin treated cells, clas...

SupramoleculeName: Human mitoribosome isolated from 1mM neomycin treated cells, class partially rotated state with A/P-site and P/E-site tRNAs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4-#86, #3
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 / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65109
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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