+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4215 | |||||||||
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Title | Yeast 80S ribosome with an uncleaved 20S rRNA | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Scaiola A / Pena C / Weisser M / Boehringer D / Leibundgut M / Klingauf-Nerurkar P / Gerhardy S / Panse VG / Ban N | |||||||||
Citation | Journal: EMBO J / Year: 2018 Title: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit. Authors: Alain Scaiola / Cohue Peña / Melanie Weisser / Daniel Böhringer / Marc Leibundgut / Purnima Klingauf-Nerurkar / Stefan Gerhardy / Vikram Govind Panse / Nenad Ban / Abstract: Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron ...Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4215.map.gz | 18.2 MB | EMDB map data format | |
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Header (meta data) | emd-4215-v30.xml emd-4215.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_4215.png | 86 KB | ||
Others | emd_4215_half_map_1.map.gz emd_4215_half_map_2.map.gz | 98.1 MB 98.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4215 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4215 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4215.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_4215_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4215_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA
Entire | Name: Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA |
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Components |
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-Supramolecule #1: Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA
Supramolecule | Name: Cytoplasmic yeast 80S ribosome with a uncleaved 20S rRNA type: complex / ID: 1 / Parent: 0 |
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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: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: OTHER |
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Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 145081 |