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Yorodumi- EMDB-10713: Early cytoplasmic yeast pre-40S particle (purified with Tsr1 as bait) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10713 | |||||||||
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Title | Early cytoplasmic yeast pre-40S particle (purified with Tsr1 as bait) | |||||||||
Map data | Cryo-EM map of yeast Tsr1-FPZ pre-40S particle. Postprocessed (LocScale), auto-refined class 1 after global classification from consensus reconstruction. | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of RNA import into nucleus / Ragulator complex / ATP export / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endocytic recycling / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling ...positive regulation of RNA import into nucleus / Ragulator complex / ATP export / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endocytic recycling / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / Protein hydroxylation / : / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to osmotic stress / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / snoRNA binding / 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 / proteasome assembly / 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 / ribonucleoprotein complex binding / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / unfolded protein binding / protein transport / late endosome / ribosome biogenesis / late endosome membrane / cellular response to oxidative stress / cytoplasmic translation / small ribosomal subunit / rRNA binding / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / structural constituent of ribosome / translation / phosphorylation / protein serine kinase activity / mRNA binding / GTPase activity / protein serine/threonine kinase activity / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Shayan R / Plassart L / Plisson-Chastang C | |||||||||
Funding support | France, 1 items
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Citation | Journal: Molecules / Year: 2020 Title: Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy. Authors: Ramtin Shayan / Dana Rinaldi / Natacha Larburu / Laura Plassart / Stéphanie Balor / David Bouyssié / Simon Lebaron / Julien Marcoux / Pierre-Emmanuel Gleizes / Célia Plisson-Chastang / Abstract: Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past ...Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past few years, characterization of the many molecular events underlying eukaryotic ribosome biogenesis has been drastically improved by the "resolution revolution" of cryo-electron microscopy (cryo-EM). However, if very early maturation events have been well characterized for both yeast ribosomal subunits, little is known regarding the final maturation steps occurring to the small (40S) ribosomal subunit. To try to bridge this gap, we have used proteomics together with cryo-EM and single particle analysis to characterize yeast pre-40S particles containing the ribosome biogenesis factor Tsr1. Our analyses lead us to refine the timing of the early pre-40S particle maturation steps. Furthermore, we suggest that after an early and structurally stable stage, the beak and platform domains of pre-40S particles enter a "vibrating" or "wriggling" stage, that might be involved in the final maturation of 18S rRNA as well as the fitting of late ribosomal proteins into their mature position. | |||||||||
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_10713.map.gz | 17.3 MB | EMDB map data format | |
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Header (meta data) | emd-10713-v30.xml emd-10713.xml | 49.6 KB 49.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10713_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_10713.png | 63.3 KB | ||
Others | emd_10713_half_map_1.map.gz emd_10713_half_map_2.map.gz | 140.4 MB 140.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10713 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10713 | HTTPS FTP |
-Related structure data
Related structure data | 6y7cMC M: atomic model generated by this map C: citing same article (ref.) |
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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_10713.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of yeast Tsr1-FPZ pre-40S particle. Postprocessed (LocScale), auto-refined class 1 after global classification from consensus reconstruction. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Cryo-EM map of yeast Tsr1-FPZ pre-40S particle. Half-map...
File | emd_10713_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM map of yeast Tsr1-FPZ pre-40S particle. Half-map 1 of auto-refined class 1 after global classification from consensus reconstruction. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM map of yeast Tsr1-FPZ pre-40S particle. Half-map...
File | emd_10713_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM map of yeast Tsr1-FPZ pre-40S particle. Half-map 1 of auto-refined class 2 after global classification from consensus reconstruction. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)
+Supramolecule #1: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait)
+Macromolecule #1: 20S ribosomal RNA
+Macromolecule #2: 40S ribosomal protein S0-A
+Macromolecule #3: 40S ribosomal protein S1-A
+Macromolecule #4: 40S ribosomal protein S2
+Macromolecule #5: 40S ribosomal protein S4-A
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S6-A
+Macromolecule #8: 40S ribosomal protein S7-A
+Macromolecule #9: 40S ribosomal protein S8-A
+Macromolecule #10: 40S ribosomal protein S9-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 S14-A
+Macromolecule #15: 40S ribosomal protein S15
+Macromolecule #16: 40S ribosomal protein S16-A
+Macromolecule #17: 40S ribosomal protein S17-A
+Macromolecule #18: 40S ribosomal protein S18-A
+Macromolecule #19: 40S ribosomal protein S19-A
+Macromolecule #20: 40S ribosomal protein S20
+Macromolecule #21: 40S ribosomal protein S21-A
+Macromolecule #22: 40S ribosomal protein S22-A
+Macromolecule #23: 40S ribosomal protein S23-A
+Macromolecule #24: 40S ribosomal protein S24-A
+Macromolecule #25: 40S ribosomal protein S25-A
+Macromolecule #26: 40S ribosomal protein S27-A
+Macromolecule #27: 40S ribosomal protein S28-A
+Macromolecule #28: 40S ribosomal protein S29-A
+Macromolecule #29: 40S ribosomal protein S30-A
+Macromolecule #30: Pre-rRNA-processing protein PNO1
+Macromolecule #31: Essential nuclear protein 1
+Macromolecule #32: Protein LTV1
+Macromolecule #33: Serine/threonine-protein kinase RIO2
+Macromolecule #34: Ribosome biogenesis protein TSR1
-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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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292 K / Instrument: LEICA EM GP |
-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 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 29.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |