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- EMDB-59080: In-cell structure of the human pre-60S state Ipre -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-59080
TitleIn-cell structure of the human pre-60S state Ipre
Map dataIn-cell structure of the human pre-60S state Ipre
Sample
  • Cell: pre-60S in native HeLa cell
Keywordsin-cell / pre-60S / human / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 8.8 Å
AuthorsZhao X / Mahamid J / Mueller CW
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: To Be Published
Title: In-cell structure of the human pre-60S state Ipre
Authors: Zhao X / Mahamid J / Mueller CW
History
DepositionJul 20, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59080.png

Downloads & links

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Map

FileDownload / File: emd_59080.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn-cell structure of the human pre-60S state Ipre
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.43 Å/pix.
x 292 pix.
= 1000.1 Å		3.43 Å/pix.
x 292 pix.
= 1000.1 Å		3.43 Å/pix.
x 292 pix.
= 1000.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.425 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.0055044093 - 0.030897746
Average (Standard dev.)-0.00006687037 (±0.0010679454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions292292292
Spacing292292292
CellA=B=C: 1000.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_59080_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In-cell structure of the human pre-60S state Ipre half1

Fileemd_59080_half_map_1.map
AnnotationIn-cell structure of the human pre-60S state Ipre half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In-cell structure of the human pre-60S state Ipre half2

Fileemd_59080_half_map_2.map
AnnotationIn-cell structure of the human pre-60S state Ipre half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pre-60S in native HeLa cell

EntireName: pre-60S in native HeLa cell
Components
  • Cell: pre-60S in native HeLa cell

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Supramolecule #1: pre-60S in native HeLa cell

SupramoleculeName: pre-60S in native HeLa cell / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/20 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp
Software - details: Tilt series were processed in Warp. Subtomograms were classified and initially refined in RELION. Final multi-particle refinement and reconstruction were performed using M (Warp/M).
Number subtomograms used: 7217
ExtractionNumber tomograms: 305 / Number images used: 1284773 / Software - Name: Warp
Software - details: Tilt series were processed in Warp. Subtomograms were classified and initially refined in RELION. Final multi-particle refinement and reconstruction were performed using M (Warp/M).
CTF correctionSoftware - Name: Warp
Software - details: Tilt series were processed in Warp. Subtomograms were classified and initially refined in RELION. Final multi-particle refinement and reconstruction were performed using M (Warp/M).
Type: PHASE FLIPPING ONLY
Final 3D classificationSoftware - Name: RELION (ver. 4.0.1)
Software - details: Tilt series were processed in Warp. Subtomograms were classified and initially refined in RELION. Final multi-particle refinement and reconstruction were performed using M (Warp/M).
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: Warp
Software - details: Tilt series were processed in Warp. Subtomograms were classified and initially refined in RELION. Final multi-particle refinement and reconstruction were performed using M (Warp/M).
FSC plot (resolution estimation)

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