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Basic information

Entry
Database: EMDB / ID: EMD-75540
TitleYeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP* - Pwp1 focused map
Map data
Sample
  • Complex: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
Keywordsribosome biogenesis / co-transcriptional assembly / RNA-binding protein / nucleolar RNP / RIBOSOME
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsPiwowarczyk R / 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: 2026
Title: Mechanism for the initiation of co-transcriptional pre-60 S assembly.
Authors: Piwowarczyk R / Klinge S
History
DepositionFeb 12, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75540.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 1.0626 Å
Density
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-55.107998000000002 - 97.309629999999999
Average (Standard dev.)0.000000000000195 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 318.78 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP

EntireName: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
Components
  • Complex: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP

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Supramolecule #1: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP

SupramoleculeName: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae S288C (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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 242741
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8e5t


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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