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- EMDB-50650: Stalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-50650
TitleStalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement
Map dataStalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement - local resolution filtered
Sample
  • Complex: Utp23-FTpA, Krr1-deltaC3
Keywords90S / pre-ribosome / snoRNA / snR30 / snoRNP / ribosome biogenesis / H/ACA / 18S rRNA / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsThoms M / Berninghausen O / Beckmann R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Commun / Year: 2025
Title: H/ACA snR30 snoRNP guides independent 18S rRNA subdomain formation.
Authors: Paulina Fischer / Matthias Thoms / Benjamin Lau / Timo Denk / Maria Kuvshinova / Otto Berninghausen / Dirk Flemming / Ed Hurt / Roland Beckmann /
Abstract: Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, ...Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, composed of pre-18S rRNA, ribosomal S-proteins, U3 snoRNA, and ~70 assembly factors. However, how numerous snoRNAs control pre-rRNA modification and folding during early maturation events remains unclear. We identify snR30 (human U17), the only essential H/ACA snoRNA in yeast, which binds with Cbf5-Gar1-Nop10-Nhp2 to a pre-18S rRNA subdomain containing platform helices and ES6 of the 40S central domain. Integration into the 90S is blocked by RNA hybridization with snR30. The snoRNP complex coordinates the recruitment of early assembly factors Krr1-Utp23-Kri1 and ribosomal proteins uS11-uS15, enabling isolated subdomain assembly. Krr1-dependent release of snR30 culminates in integration of the platform into the 90S. Our study reveals the essential role of snR30 in chaperoning central domain formation as a discrete assembly unit externalized from the pre-ribosomal core.
History
DepositionJun 15, 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_50650.png

Downloads & links

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Map

FileDownload / File: emd_50650.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement - local resolution filtered
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.40823 - 5.155735
Average (Standard dev.)0.0026110064 (±0.052922133)
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: Stalled 90S - Utp23-Krr1-deltaC3 - Nop14 module -...

Fileemd_50650_additional_1.map
AnnotationStalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement - sharpened
Projections & Slices
AxesZYX

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Histogram

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Additional map: Stalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement

Fileemd_50650_additional_2.map
AnnotationStalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Stalled 90S - Utp23-Krr1-deltaC3 - Nop14 module -...

Fileemd_50650_half_map_1.map
AnnotationStalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement - half map B
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Stalled 90S - Utp23-Krr1-deltaC3 - Nop14 module -...

Fileemd_50650_half_map_2.map
AnnotationStalled 90S - Utp23-Krr1-deltaC3 - Nop14 module - local refinement - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Utp23-FTpA, Krr1-deltaC3

EntireName: Utp23-FTpA, Krr1-deltaC3
Components
  • Complex: Utp23-FTpA, Krr1-deltaC3

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Supramolecule #1: Utp23-FTpA, Krr1-deltaC3

SupramoleculeName: Utp23-FTpA, Krr1-deltaC3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#65
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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: 46.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32278
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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