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- EMDB-50958: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - local ref... -

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Basic information

Entry
Database: EMDB / ID: EMD-50958
TitlesnR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - local refinement
Map datasnR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - 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: 2.83 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
DepositionJul 10, 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_50958.png

Downloads & links

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Map

FileDownload / File: emd_50958.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationsnR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - local refinement - local resolution filtered
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.9385562 - 6.1915207
Average (Standard dev.)0.0014849947 (±0.06961148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 -...

Fileemd_50958_additional_1.map
AnnotationsnR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - local refinement
Projections & Slices
AxesZYX

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Additional map: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 -...

Fileemd_50958_additional_2.map
AnnotationsnR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - local refinement - sharpened
Projections & Slices
AxesZYX

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Half map: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 -...

Fileemd_50958_half_map_1.map
AnnotationsnR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - local refinement - half map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: snR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 -...

Fileemd_50958_half_map_2.map
AnnotationsnR30 snoRNP - State 1 - Utp23-Krr1-deltaC3 - 3' HACA - local refinement - half map B
Projections & Slices
AxesZYX

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Slices (1/2)
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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
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171224
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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