[English] 日本語
Yorodumi- EMDB-21644: Subunit joining exposes nascent pre-40S rRNA for processing and q... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21644 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Subunit joining exposes nascent pre-40S rRNA for processing and quality control | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Function / homology | Function and homology information endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation ...endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / U3 snoRNA binding / : / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / G-protein alpha-subunit binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / positive regulation of protein kinase activity / ribonucleoprotein complex binding / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / ribosome binding / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Rai J / Parker MD / Huang H / Choy S / Ghalei H / Johnson MC / Karbstein K / Stroupe ME | ||||||||||||
Funding support | United States, 3 items
| ||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21644.map.gz | 120.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-21644-v30.xml emd-21644.xml | 49.7 KB 49.7 KB | Display Display | EMDB header |
Images | emd_21644.png | 172.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21644 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21644 | HTTPS FTP |
-Related structure data
Related structure data | 6wdrMC 6oigC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_21644.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : 80S-like ribosome
+Supramolecule #1: 80S-like ribosome
+Macromolecule #1: 40S ribosomal protein S0-A
+Macromolecule #2: 40S ribosomal protein S2
+Macromolecule #3: 40S ribosomal protein S3
+Macromolecule #4: 40S ribosomal protein S4-A
+Macromolecule #5: 40S ribosomal protein S5
+Macromolecule #6: 40S ribosomal protein S6-A
+Macromolecule #7: 40S ribosomal protein S7-A
+Macromolecule #8: 40S ribosomal protein S8-A
+Macromolecule #9: 40S ribosomal protein S9-A
+Macromolecule #10: 40S ribosomal protein S10-A
+Macromolecule #11: 40S ribosomal protein S11-A
+Macromolecule #12: 40S ribosomal protein S12
+Macromolecule #13: 40S ribosomal protein S13
+Macromolecule #14: 40S ribosomal protein S15
+Macromolecule #15: 40S ribosomal protein S16-A
+Macromolecule #16: 40S ribosomal protein S17-A
+Macromolecule #17: 40S ribosomal protein S18-A
+Macromolecule #18: 40S ribosomal protein S19-A
+Macromolecule #19: 40S ribosomal protein S20
+Macromolecule #20: 40S ribosomal protein S21-A
+Macromolecule #21: 40S ribosomal protein S22-A
+Macromolecule #22: 40S ribosomal protein S23-A
+Macromolecule #23: 40S ribosomal protein S24-A
+Macromolecule #24: 40S ribosomal protein S25-A
+Macromolecule #25: 40S ribosomal protein S27-A
+Macromolecule #26: 40S ribosomal protein S28-A
+Macromolecule #27: 40S ribosomal protein S29-A
+Macromolecule #28: 40S ribosomal protein S30-A
+Macromolecule #29: Ubiquitin-40S ribosomal protein S31
+Macromolecule #30: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #31: Ribosome biogenesis protein TSR1
+Macromolecule #32: 20S ribosomal RNA
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
---|---|
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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) / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing #1
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
---|---|
Final angle assignment | Type: OTHER |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90692 |
Image processing ID | 1 |
-Image processing #2
Initial angle assignment | Type: OTHER |
---|---|
Final angle assignment | Type: OTHER |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90692 |
Image processing ID | 2 |
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | PDB-6wdr: |