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- EMDB-48963: SSU processome maturation and disassembly, State D - Bfr2Kre33 fo... -

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Basic information

Entry
Database: EMDB / ID: EMD-48963
TitleSSU processome maturation and disassembly, State D - Bfr2Kre33 focused map
Map data
Sample
  • Complex: SSU processome maturation and disassembly, State D
KeywordsSSU processome / ribosome assembly / RNA folding / RNA-protein interactions / RIBOSOME
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.76 Å
AuthorsBuzovetsky O / Klinge S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM145950-03 United States
Chan Zuckerberg Initiative2023-332391 United States
CitationJournal: Nature / Year: 2025
Title: Helicase-mediated mechanism of SSU processome maturation and disassembly.
Authors: Olga Buzovetsky / Sebastian Klinge /
Abstract: Eukaryotic ribosomal small subunit (SSU) assembly requires the SSU processome, a nucleolar precursor containing the RNA chaperone U3 small nucleolar RNA (snoRNA). The underlying molecular mechanisms ...Eukaryotic ribosomal small subunit (SSU) assembly requires the SSU processome, a nucleolar precursor containing the RNA chaperone U3 small nucleolar RNA (snoRNA). The underlying molecular mechanisms of SSU processome maturation, remodelling, disassembly and RNA quality control, and the transitions between states remain unknown owing to a paucity of intermediates. Here we report 16 native SSU processome structures alongside genetic data, revealing how two helicases, the Mtr4-exosome and Dhr1, are controlled for accurate and unidirectional ribosome biogenesis. Our data show how irreversible pre-ribosomal RNA degradation by the redundantly tethered RNA exosome couples the transformation of the SSU processome into a pre-40S particle, during which Utp14 can probe evolving surfaces, ultimately positioning and activating Dhr1 to unwind the U3 snoRNA and initiate nucleolar pre-40S release. This study highlights a paradigm for large dynamic RNA-protein complexes in which irreversible RNA degradation drives compositional changes and communicates these changes to govern enzyme activity while maintaining overall quality control.
History
DepositionFeb 4, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48963.png

Downloads & links

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Map

FileDownload / File: emd_48963.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 504 pix.
= 535.752 Å		1.06 Å/pix.
x 504 pix.
= 535.752 Å		1.06 Å/pix.
x 504 pix.
= 535.752 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.524
Minimum - Maximum-0.8829289 - 1.5195109
Average (Standard dev.)0.006271953 (±0.060884006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 535.75195 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48963_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_48963_half_map_1.map
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Half map: #2

Fileemd_48963_half_map_2.map
Projections & Slices
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Sample components

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Entire : SSU processome maturation and disassembly, State D

EntireName: SSU processome maturation and disassembly, State D
Components
  • Complex: SSU processome maturation and disassembly, State D

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Supramolecule #1: SSU processome maturation and disassembly, State D

SupramoleculeName: SSU processome maturation and disassembly, State D / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#68
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (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
Component:
ConcentrationName
60.0 mMTris-HCl
50.0 mMNaCl
5.0 mMMgCl
2.0 %glycerol
0.01 %NP-40
1.0 mMDTT
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 1.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12826
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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