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Yorodumi- EMDB-30113: Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30113 | ||||||||||||
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Title | Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisiae Sda1 depletion strain, E1 state | ||||||||||||
Map data | Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisiae Sda1 depletion strain, E1 state | ||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | ||||||||||||
Authors | Li Y / Micic J | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly. Authors: Jelena Micic / Yu Li / Shan Wu / Daniel Wilson / Beril Tutuncuoglu / Ning Gao / John L Woolford / Abstract: The protein composition and structure of assembling 60S ribosomal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleoplasm. This includes stable anchoring ...The protein composition and structure of assembling 60S ribosomal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleoplasm. This includes stable anchoring of the Rpf2 subcomplex containing 5S rRNA, rpL5, rpL11, Rpf2 and Rrs1, which initially docks onto the flexible domain V of rRNA at earlier stages of assembly. In this work, we tested the function of the C-terminal domain (CTD) of Rpf2 during these anchoring steps, by truncating this extension and assaying effects on middle stages of subunit maturation. The rpf2Δ255-344 mutation affects proper folding of rRNA helices H68-70 during anchoring of the Rpf2 subcomplex. In addition, several assembly factors (AFs) are absent from pre-ribosomes or in altered conformations. Consequently, major remodeling events fail to occur: rotation of the 5S RNP, maturation of the peptidyl transferase center (PTC) and the nascent polypeptide exit tunnel (NPET), and export of assembling subunits to the cytoplasm. | ||||||||||||
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_30113.map.gz | 226 MB | EMDB map data format | |
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Header (meta data) | emd-30113-v30.xml emd-30113.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_30113.png | 50.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30113 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30113 | HTTPS FTP |
-Validation report
Summary document | emd_30113_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_30113_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_30113_validation.xml.gz | 491 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30113 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30113 | 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_30113.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisiae Sda1 depletion strain, E1 state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.057 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi...
Entire | Name: Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisiae Sda1 depletion strain, E1 state |
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Components |
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-Supramolecule #1: Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi...
Supramolecule | Name: Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisiae Sda1 depletion strain, E1 state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#58 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (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: 1.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50552 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |