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- EMDB-43026: 60S ribosome biogenesis intermediate (Dbp10 catalytic intermediat... -

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Basic information

Entry
Database: EMDB / ID: EMD-43026
Title60S ribosome biogenesis intermediate (Dbp10 catalytic intermediate - Rrp14/Rrp15/Ssf1 local map)
Map dataLocal refined half Ssf1 region
Sample
  • Complex: 60S ribosome biogenesis intermediate
KeywordsRibosome biogenesis intermediate DEAD-box ATPase / RIBOSOME
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsCruz VE / Weirich CS / Peddada N / Erzberger JP
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM135617-01 United States
Robert A. Welch FoundationI-1897 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150074 United States
CitationJournal: Nat Commun / Year: 2024
Title: The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
Authors: Victor E Cruz / Christine S Weirich / Nagesh Peddada / Jan P Erzberger /
Abstract: DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this ...DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this study, we present cryo-EM reconstructions of nucleolar pre-60S intermediates that reveal an unexpected, alternate secondary structure within the nascent peptidyl-transferase-center (PTC). Our analysis of three sequential nucleolar pre-60S intermediates reveals that the DEAD-box ATPase Dbp10/DDX54 remodels this alternate base pairing and enables the formation of the rRNA junction that anchors the mature form of the universally conserved PTC A-loop. Post-catalysis, Dbp10 captures rRNA helix H61, initiating the concerted exchange of biogenesis factors during late nucleolar 60S maturation. Our findings show that Dbp10 activity is essential for the formation of the ribosome active site and reveal how this function is integrated with subsequent assembly steps to drive the biogenesis of the large ribosomal subunit.
History
DepositionDec 4, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43026.png

Downloads & links

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Map

FileDownload / File: emd_43026.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refined half Ssf1 region
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.034042474 - 0.08641485
Average (Standard dev.)0.000017889379 (±0.0017296724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Local refined half map 2 Ssf1 region

Fileemd_43026_half_map_1.map
AnnotationLocal refined half map 2 Ssf1 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Local refined half map 1 Ssf1 region

Fileemd_43026_half_map_2.map
AnnotationLocal refined half map 1 Ssf1 region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 60S ribosome biogenesis intermediate

EntireName: 60S ribosome biogenesis intermediate
Components
  • Complex: 60S ribosome biogenesis intermediate

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Supramolecule #1: 60S ribosome biogenesis intermediate

SupramoleculeName: 60S ribosome biogenesis intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#48
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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6em1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 179000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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