+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16276 | ||||||||||||
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Title | Release state - ES27up (pre-60S) | ||||||||||||
Map data | Composite map | ||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||
Authors | Thoms M / Mitterer V / Buschauer R / Berninghausen O / Hurt E / Beckmann R | ||||||||||||
Funding support | Germany, European Union, 3 items
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Citation | Journal: Elife / Year: 2023 Title: Concurrent remodelling of nucleolar 60S subunit precursors by the Rea1 ATPase and Spb4 RNA helicase. Authors: Valentin Mitterer / Matthias Thoms / Robert Buschauer / Otto Berninghausen / Ed Hurt / Roland Beckmann / Abstract: Biogenesis intermediates of nucleolar ribosomal 60S precursor particles undergo a number of structural maturation steps before they transit to the nucleoplasm and are finally exported into the ...Biogenesis intermediates of nucleolar ribosomal 60S precursor particles undergo a number of structural maturation steps before they transit to the nucleoplasm and are finally exported into the cytoplasm. The AAA-ATPase Rea1 participates in the nucleolar exit by releasing the Ytm1-Erb1 heterodimer from the evolving pre-60S particle. Here, we show that the DEAD-box RNA helicase Spb4 with its interacting partner Rrp17 is further integrated into this maturation event. Spb4 binds to a specific class of late nucleolar pre-60S intermediates, whose cryo-EM structure revealed how its helicase activity facilitates melting and restructuring of 25S rRNA helices H62 and H63/H63a prior to Ytm1-Erb1 release. In vitro maturation of such Spb4-enriched pre-60S particles, incubated with purified Rea1 and its associated pentameric Rix1-complex in the presence of ATP, combined with cryo-EM analysis depicted the details of the Rea1-dependent large-scale pre-ribosomal remodeling. Our structural insights unveil how the Rea1 ATPase and Spb4 helicase remodel late nucleolar pre-60S particles by rRNA restructuring and dismantling of a network of several ribosomal assembly factors. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16276.map.gz | 19.7 MB | EMDB map data format | |
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Header (meta data) | emd-16276-v30.xml emd-16276.xml | 34.7 KB 34.7 KB | Display Display | EMDB header |
Images | emd_16276.png | 87.4 KB | ||
Others | emd_16276_additional_1.map.gz emd_16276_additional_2.map.gz emd_16276_additional_3.map.gz emd_16276_additional_4.map.gz emd_16276_additional_5.map.gz emd_16276_additional_6.map.gz emd_16276_additional_7.map.gz emd_16276_half_map_1.map.gz emd_16276_half_map_2.map.gz | 6.6 MB 8.4 MB 7.1 MB 2.5 MB 21.7 MB 239.6 MB 450.2 MB 442 MB 442 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16276 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16276 | HTTPS FTP |
-Validation report
Summary document | emd_16276_validation.pdf.gz | 809.5 KB | Display | EMDB validaton report |
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Full document | emd_16276_full_validation.pdf.gz | 809 KB | Display | |
Data in XML | emd_16276_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_16276_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16276 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16276 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16276.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Foot - Local Refinement - Local filtered map
File | emd_16276_additional_1.map | ||||||||||||
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Annotation | Foot - Local Refinement - Local filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: ES27 - Local Refinement - Local filtered map
File | emd_16276_additional_2.map | ||||||||||||
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Annotation | ES27 - Local Refinement - Local filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Nog1 - Local Refinement - Local filtered map
File | emd_16276_additional_3.map | ||||||||||||
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Annotation | Nog1 - Local Refinement - Local filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Spb1-MTD - Local Refinement - Local filtered map
File | emd_16276_additional_4.map | ||||||||||||
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Annotation | Spb1-MTD - Local Refinement - Local filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus cryo-EM map - Local filtered map
File | emd_16276_additional_5.map | ||||||||||||
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Annotation | Consensus cryo-EM map - Local filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus cryo-EM map - Homogeneous Refinement
File | emd_16276_additional_6.map | ||||||||||||
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Annotation | Consensus cryo-EM map - Homogeneous Refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus cryo-EM map - Homogeneous Refinement - sharpened map
File | emd_16276_additional_7.map | ||||||||||||
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Annotation | Consensus cryo-EM map - Homogeneous Refinement - sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Consensus cryo-EM map - half map A
File | emd_16276_half_map_1.map | ||||||||||||
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Annotation | Consensus cryo-EM map - half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Consensus cryo-EM map - half map B
File | emd_16276_half_map_2.map | ||||||||||||
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Annotation | Consensus cryo-EM map - half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Release state - ES27up (pre-60S)
Entire | Name: Release state - ES27up (pre-60S) |
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Components |
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-Supramolecule #1: Release state - ES27up (pre-60S)
Supramolecule | Name: Release state - ES27up (pre-60S) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#60 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 46.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29118 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |