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- EMDB-48937: SSU processome maturation and disassembly, State A - UtpC focused map -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-48937
TitleSSU processome maturation and disassembly, State A - UtpC focused map
Map data
Sample
  • Complex: SSU processome maturation and disassembly, State A
KeywordsSSU processome / ribosome assembly / RNA folding / RNA-protein interactions / RIBOSOME
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 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: bioRxiv / 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 snoRNA. The underlying molecular mechanisms of SSU processome ...Eukaryotic ribosomal small subunit (SSU) assembly requires the SSU processome, a nucleolar precursor containing the RNA chaperone U3 snoRNA. The underlying molecular mechanisms of SSU processome maturation, remodeling, disassembly, RNA quality control, and the transitions between states remain elusive due 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-40 particle during which Utp14 can probe evolving surfaces, ultimately positioning and activating Dhr1 to unwind the U3 snoRNA and initiate nucleolar pre-40 release. This study highlights a paradigm for large dynamic RNA-protein complexes where 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-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48937.png

Downloads & links

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Map

FileDownload / File: emd_48937.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7278
Minimum - Maximum-2.2058482 - 3.5828316
Average (Standard dev.)0.00833179 (±0.10603732)
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_48937_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #1

Fileemd_48937_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48937_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : SSU processome maturation and disassembly, State A

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

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

SupramoleculeName: SSU processome maturation and disassembly, State A / 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: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36965
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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