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- EMDB-34285: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -

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Basic information

Entry
Database: EMDB / ID: EMD-34285
TitleCryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae (Nop14 5Ala, Cms1 KO), state B2
Map data
Sample
  • Complex: 90S pre-ribosome
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsCheng J / Lau B / Hurt E / Beckmann R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: Cms1 coordinates stepwise local 90S pre-ribosome assembly with timely snR83 release.
Authors: Benjamin Lau / Olga Beine-Golovchuk / Markus Kornprobst / Jingdong Cheng / Dieter Kressler / Beáta Jády / Tamás Kiss / Roland Beckmann / Ed Hurt /
Abstract: Ribosome synthesis begins in the nucleolus with 90S pre-ribosome construction, but little is known about how the many different snoRNAs that modify the pre-rRNA are timely guided to their target ...Ribosome synthesis begins in the nucleolus with 90S pre-ribosome construction, but little is known about how the many different snoRNAs that modify the pre-rRNA are timely guided to their target sites. Here, we report a role for Cms1 in such a process. Initially, we discovered CMS1 as a null suppressor of a nop14 mutant impaired in Rrp12-Enp1 factor recruitment to the 90S. Further investigations detected Cms1 at the 18S rRNA 3' major domain of an early 90S that carried H/ACA snR83, which is known to guide pseudouridylation at two target sites within the same subdomain. Cms1 co-precipitates with many 90S factors, but Rrp12-Enp1 encircling the 3' major domain in the mature 90S is decreased. We suggest that Cms1 associates with the 3' major domain during early 90S biogenesis to restrict premature Rrp12-Enp1 binding but allows snR83 to timely perform its modification role before the next 90S assembly steps coupled with Cms1 release take place.
History
DepositionSep 14, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34285.png

Downloads & links

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Map

FileDownload / File: emd_34285.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 480 pix.
= 501.6 Å		1.05 Å/pix.
x 480 pix.
= 501.6 Å		1.05 Å/pix.
x 480 pix.
= 501.6 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: 0.02
Minimum - Maximum-0.18761237 - 0.2946853
Average (Standard dev.)0.0004693015 (±0.0077377805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 501.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34285_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_34285_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : 90S pre-ribosome

EntireName: 90S pre-ribosome
Components
  • Complex: 90S pre-ribosome

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Supramolecule #1: 90S pre-ribosome

SupramoleculeName: 90S pre-ribosome / type: complex / Chimera: Yes / 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: 7.4
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: 44.0 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33340
Initial angle assignmentType: OTHER / Details: Relion
Final angle assignmentType: OTHER / Details: Relion
FSC plot (resolution estimation)

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