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Yorodumi- EMDB-20077: Subunit joining exposes nascent pre-40S rRNA for processing and q... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20077 | ||||||||||||
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Title | Subunit joining exposes nascent pre-40S rRNA for processing and quality control | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | 80S-like complex / 60S / RIBOSOME | ||||||||||||
Function / homology | Function and homology information pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome ...pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / translational termination / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / ribosomal large subunit assembly / protein tag activity / rRNA processing / large ribosomal subunit rRNA binding / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Rai J / Parker MD | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: RNA / Year: 2021 Title: An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7. Authors: Jay Rai / Melissa D Parker / Haina Huang / Stefan Choy / Homa Ghalei / Matthew C Johnson / Katrin Karbstein / M Elizabeth Stroupe / Abstract: During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly ...During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly intermediates are essential for maturation and quality control, how they form, and how their structure promotes quality control, remains unknown. To address these questions, we determined the structure of an 80S-like ribosome assembly intermediate to an overall resolution of 3.4 Å. The structure, validated by biochemical data, resolves a large body of previously paradoxical data and illustrates how assembly and translation factors cooperate to promote the formation of an interface that lacks many mature subunit contacts but is stabilized by the universally conserved methyltransferase Dim1. We also show how Tsr1 enables this interface by blocking the canonical binding of eIF5B to 40S subunits, while maintaining its binding to 60S. The structure also shows how this interface leads to unfolding of the platform, which allows for temporal regulation of the ATPase Fap7, thus linking 40S maturation to quality control during ribosome assembly. | ||||||||||||
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_20077.map.gz | 121.5 MB | EMDB map data format | |
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Header (meta data) | emd-20077-v30.xml emd-20077.xml | 68.8 KB 68.8 KB | Display Display | EMDB header |
Images | emd_20077.png | 146.6 KB | ||
Filedesc metadata | emd-20077.cif.gz | 13.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20077 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20077 | HTTPS FTP |
-Related structure data
Related structure data | 6oigMC 6wdrC C: citing same article (ref.) M: atomic model generated by this map |
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Similar 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_20077.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.24 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 : 60S subunit of 80S-like ribosome
+Supramolecule #1: 60S subunit of 80S-like ribosome
+Macromolecule #1: 60S ribosomal protein L1-A
+Macromolecule #2: 60S ribosomal protein L2-A
+Macromolecule #3: 60S ribosomal protein L3
+Macromolecule #4: 60S ribosomal protein L4-A
+Macromolecule #5: 60S ribosomal protein L5
+Macromolecule #6: 60S ribosomal protein L6-A
+Macromolecule #7: 60S ribosomal protein L7-A
+Macromolecule #8: 60S ribosomal protein L8-A
+Macromolecule #9: 60S ribosomal protein L9-A
+Macromolecule #10: 60S ribosomal protein L10
+Macromolecule #11: 60S ribosomal protein L11-B
+Macromolecule #12: 60S ribosomal protein L12-A
+Macromolecule #13: 60S ribosomal protein L13-A
+Macromolecule #14: 60S ribosomal protein L14-A
+Macromolecule #15: 60S ribosomal protein L15-A
+Macromolecule #16: 60S ribosomal protein L16-A
+Macromolecule #17: 60S ribosomal protein L17-A
+Macromolecule #18: 60S ribosomal protein L18-A
+Macromolecule #19: 60S ribosomal protein L19-A
+Macromolecule #20: 60S ribosomal protein L20-A
+Macromolecule #21: 60S ribosomal protein L21-A
+Macromolecule #22: 60S ribosomal protein L22-A
+Macromolecule #23: 60S ribosomal protein L23-A
+Macromolecule #24: 60S ribosomal protein L24-A
+Macromolecule #25: 60S ribosomal protein L25
+Macromolecule #26: 60S ribosomal protein L26-A
+Macromolecule #27: 60S ribosomal protein L27-A
+Macromolecule #28: 60S ribosomal protein L28
+Macromolecule #29: 60S ribosomal protein L29
+Macromolecule #30: 60S ribosomal protein L30
+Macromolecule #31: 60S ribosomal protein L31-A
+Macromolecule #32: 60S ribosomal protein L32
+Macromolecule #33: 60S ribosomal protein L33-A
+Macromolecule #34: 60S ribosomal protein L34-A
+Macromolecule #35: 60S ribosomal protein L35-A
+Macromolecule #36: 60S ribosomal protein L36-A
+Macromolecule #37: 60S ribosomal protein L37-A
+Macromolecule #38: 60S ribosomal protein L38
+Macromolecule #39: 60S ribosomal protein L39
+Macromolecule #40: Ubiquitin-60S ribosomal protein L40
+Macromolecule #41: 60S ribosomal protein L42-A
+Macromolecule #42: 60S ribosomal protein L43-A
+Macromolecule #43: 60S acidic ribosomal protein P0,60S acidic ribosomal protein P0,A...
+Macromolecule #47: P1
+Macromolecule #48: P2
+Macromolecule #44: 25S ribosomal RNA
+Macromolecule #45: 5.8S ribosomal RNA
+Macromolecule #46: 5S ribosomal RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83558 |