EMDB-59075: In-cell structure of the human pre-60S state G*

Basic information

Entry

Database: EMDB / ID: EMD-59075

• Title: In-cell structure of the human pre-60S state G*
• Map data: In-cell structure of the human pre-60S state G*

Sample

• Cell: pre-60S in native HeLa cell

• Keywords: in-cell / pre-60S / human / RIBOSOME
• Biological species: Homo sapiens (human)
• Method: subtomogram averaging / cryo EM / Resolution: 9.5 Å
• Authors: Zhao X / Mahamid J / Mueller CW

Funding support

Germany, 1 items

Organization	Grant number	Country
Other government		Germany

• Citation: Journal: Science / Year: 2026; Title: In-cell structures visualize human pre-ribosome assembly in the nucleolus.; Authors: Xiaohan Zhao / Yuki Hayashi / Herman K H Fung / Sara Cuylen-Haering / Julia Mahamid / Christoph W Müller / ; Abstract: In eukaryotes, ribosome biogenesis initiates within the nucleolus, a hallmark multilayered compartment of the nucleus. Structures of pre-ribosomes have been characterized ex situ, but their assembly pathways within human nucleoli have not been described. Here, we used cryogenic correlative light and electron tomography to visualize molecular landscapes within HeLa cell nucleoli and obtained in-cell structural snapshots of both ribosomal subunit precursors, the SSU processome and the pre-60S. These recapitulate major states resolved previously ex situ and reveal additional critical interaction partners, including the RNA exosome, rixosome, and nuclear export receptor CRM1-RanGTP. We further show how pre-ribosome assembly landscapes are altered upon RNA polymerase I inhibition. Our study combines molecular structures with cellular context to elucidate the spatiotemporal assembly pathway of the human ribosome.

History

Deposition	Jul 20, 2026	-
Header (metadata) release	Sep 23, 2026	-
Map release	Sep 23, 2026	-
Update	Oct 7, 2026	-
Current status	Oct 7, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_59075.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: In-cell structure of the human pre-60S state G*
• Voxel size: X=Y=Z: 3.425 Å

Density

Contour Level	By AUTHOR: 0.008
Minimum - Maximum	-0.0047933767 - 0.029708374
Average (Standard dev.)	-0.000039300794 (±0.000937185)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 292 292 292 Spacing 292 292 292
Cell	A=B=C: 1000.1 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_59075_msk_1.map

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

• File: emd_59075_half_map_1.map
• Annotation: In-cell structure of the human pre-60S state G* half1

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

• File: emd_59075_half_map_2.map
• Annotation: In-cell structure of the human pre-60S state G* half2

Sample components

Entire : pre-60S in native HeLa cell

• Entire: Name: pre-60S in native HeLa cell

Components

• Cell: pre-60S in native HeLa cell

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

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

Experimental details

Structure determination

• Method: cryo EM
• Processing: subtomogram averaging
• Aggregation state: cell

Sample preparation

• Buffer: pH: 7.4
• Grid: Model: Quantifoil R1.2/20 / Material: GOLD / Mesh: 200 / Support film - Material: SILICON DIOXIDE
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.41 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination 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

Image processing

• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.5 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: 6553
• Extraction: Number 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 correction: 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).; Type: PHASE FLIPPING ONLY
• Final 3D classification: Software - 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 assignment: Type: 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).