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- EMDB-75541: Yeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP* ... -

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Basic information

Entry
Database: EMDB / ID: EMD-75541
TitleYeast co-transcriptional pre-60S assembly intermediate Pwp1 RNP* - Rpl8 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: 2.57 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 assembly.
Authors: Rafal Piwowarczyk / Sebastian Klinge
Abstract: Eukaryotic ribosomal large subunit (60 ) assembly requires an internal transcribed spacer 2 (ITS2) to license both nucleolar and nuclear pre-60 assembly intermediates. The underlying molecular ...Eukaryotic ribosomal large subunit (60 ) assembly requires an internal transcribed spacer 2 (ITS2) to license both nucleolar and nuclear pre-60 assembly intermediates. The underlying molecular mechanisms responsible for nucleation of pre-60 assembly, quality control, and installation of ITS2 during co-transcriptional stages remain unknown. Here we report the earliest co-transcriptional assembly intermediates of the eukaryotic 60 subunits. Together with biochemical assays, our data reveal the architecture of co-transcriptional pre-60 assembly initiation and progression, as well as the molecular logic of an assembly checkpoint. This study highlights an evolutionary solution by which complex RNA folding processes can be parallelized and integrated via biological AND-gating.
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_75541.png

Downloads & links

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Map

FileDownload / File: emd_75541.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 300 pix.
= 318.78 Å		1.06 Å/pix.
x 300 pix.
= 318.78 Å		1.06 Å/pix.
x 300 pix.
= 318.78 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0626 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-40.391959999999997 - 83.694609999999997
Average (Standard dev.)-0.00000000000187 (±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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Half map: #1

Fileemd_75541_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75541_half_map_2.map
Projections & Slices
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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: 2.57 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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