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- EMDB-27910: Yeast nucleolar Noc2-Noc3 RNP pre-60S assembly intermediate (state E) -

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Basic information

Entry
Database: EMDB / ID: EMD-27910
TitleYeast nucleolar Noc2-Noc3 RNP pre-60S assembly intermediate (state E)
Map data
Sample
  • Complex: Nucleolar large ribosomal subunit (pre-60S) assembly intermediate (state E)
KeywordsNucleolar pre-60S / ribosome biogenesis / RIBOSOME
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsSanghai ZA
Funding support United States, 2 items
OrganizationGrant numberCountry
The G. Harold and Leila Y. Mathers FoundationMF-2104-01554 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143181 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation.
Authors: Zahra A Sanghai / Rafal Piwowarczyk / Arnaud Vanden Broeck / Sebastian Klinge /
Abstract: During transcription of eukaryotic ribosomal DNA in the nucleolus, assembly checkpoints exist that guarantee the formation of stable precursors of small and large ribosomal subunits. While the ...During transcription of eukaryotic ribosomal DNA in the nucleolus, assembly checkpoints exist that guarantee the formation of stable precursors of small and large ribosomal subunits. While the formation of an early large subunit assembly checkpoint precedes the separation of small and large subunit maturation, its mechanism of action and function remain unknown. Here, we report the cryo-electron microscopy structure of the yeast co-transcriptional large ribosomal subunit assembly intermediate that serves as a checkpoint. The structure provides the mechanistic basis for how quality-control pathways are established through co-transcriptional ribosome assembly factors, that structurally interrogate, remodel and, together with ribosomal proteins, cooperatively stabilize correctly folded pre-ribosomal RNA. Our findings thus provide a molecular explanation for quality control during eukaryotic ribosome assembly in the nucleolus.
History
DepositionAug 20, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateMay 31, 2023-
Current statusMay 31, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27910.png

Downloads & links

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Map

FileDownload / File: emd_27910.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 440 pix.
= 572. Å		1.3 Å/pix.
x 440 pix.
= 572. Å		1.3 Å/pix.
x 440 pix.
= 572. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.313
Minimum - Maximum-0.70756257 - 1.6334432
Average (Standard dev.)0.0017565407 (±0.056284875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 572.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27910_half_map_1.map
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Half map: #2

Fileemd_27910_half_map_2.map
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Sample components

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Entire : Nucleolar large ribosomal subunit (pre-60S) assembly intermediate...

EntireName: Nucleolar large ribosomal subunit (pre-60S) assembly intermediate (state E)
Components
  • Complex: Nucleolar large ribosomal subunit (pre-60S) assembly intermediate (state E)

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Supramolecule #1: Nucleolar large ribosomal subunit (pre-60S) assembly intermediate...

SupramoleculeName: Nucleolar large ribosomal subunit (pre-60S) assembly intermediate (state E)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Molecular weightTheoretical: 2 MDa

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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

Concentration0.1 mg/mL
BufferpH: 7.6
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 0.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.184 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.2) / Number images used: 75358
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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