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- EMDB-19309: Human pre-60S - State 3 - 5S RNP - NLE1 - local refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-19309
TitleHuman pre-60S - State 3 - 5S RNP - NLE1 - local refinement
Map dataHuman pre-60S - State 3 - 5S RNP - NLE1 - local refinement - local resolution filtered
Sample
  • Complex: Human pre-60S - State 3 - 5S RNP - NLE1 - local refinement
KeywordsHuman / ribosome biogenesis / NLE1 / RIX1 complex / 5S RNP / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsThoms M / Denk T / Beckmann R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Citation
Journal: Nucleic Acids Res / Year: 2025
Title: Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits.
Authors: Federica Fiorentino / Matthias Thoms / Klemens Wild / Timo Denk / Jingdong Cheng / Jakub Zeman / Irmgard Sinning / Ed Hurt / Roland Beckmann /
Abstract: The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ...The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ribosome biogenesis between yeast and humans, illustrated by the structural similarities of ribosomal subunit intermediates. By using X-ray crystallography and cryo-EM, the interaction between the human AAA+ ATPase MDN1 and the 60S assembly factor NLE1 is compared with the yeast homologs Rea1 and Rsa4. The MDN1-MIDAS and NLE1-Ubl complex structure at 2.3 Å resolution mirrors the highly conserved interaction patterns observed in yeast. Moreover, human pre-60S intermediates bound to the dominant negative NLE1-E85A mutant revealed at 2.8 Å resolution an architecture that largely matched the equivalent yeast structures. Conformation of rRNA, assembly factors and their interaction networks are highly conserved. Additionally, novel human pre-60S intermediates with a non-rotated 5S RNP and processed ITS2/foot structure but incomplete intersubunit surface were identified to be similar to counterparts observed in yeast. These findings confirm that the MDN1-NLE1-driven transition phase of the 60S assembly is essentially identical, supporting the idea that ribosome biogenesis is a highly conserved process across eukaryotic cells, employing an evolutionary preservation of ribosomal assembly mechanisms.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Adams PD
History
DepositionJan 2, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19309.png

Downloads & links

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Map

FileDownload / File: emd_19309.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman pre-60S - State 3 - 5S RNP - NLE1 - local refinement - local resolution filtered
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 500 pix.
= 522.5 Å		1.05 Å/pix.
x 500 pix.
= 522.5 Å		1.05 Å/pix.
x 500 pix.
= 522.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.137208 - 3.8579514
Average (Standard dev.)0.0010748564 (±0.039204028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 522.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Human pre-60S - State 3 - 5S RNP - NLE1 - local refinement

Fileemd_19309_additional_1.map
AnnotationHuman pre-60S - State 3 - 5S RNP - NLE1 - local refinement
Projections & Slices
AxesZYX

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Half map: Human pre-60S - State 3 - 5S RNP...

Fileemd_19309_half_map_1.map
AnnotationHuman pre-60S - State 3 - 5S RNP - NLE1 - local refinement - half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Human pre-60S - State 3 - 5S RNP...

Fileemd_19309_half_map_2.map
AnnotationHuman pre-60S - State 3 - 5S RNP - NLE1 - local refinement - half map B
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 pre-60S - State 3 - 5S RNP - NLE1 - local refinement

EntireName: Human pre-60S - State 3 - 5S RNP - NLE1 - local refinement
Components
  • Complex: Human pre-60S - State 3 - 5S RNP - NLE1 - local refinement

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Supramolecule #1: Human pre-60S - State 3 - 5S RNP - NLE1 - local refinement

SupramoleculeName: Human pre-60S - State 3 - 5S RNP - NLE1 - local refinement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#40
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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33891
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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