+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4793 | |||||||||
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Title | State 2 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles | |||||||||
Map data | Yeast pre-40S particle, purified using Tsr1-TAP as bait, in mutant conditions (deletion of aa 68-78 of Rps20) Structural class 2 Final EM map; local sharpening with LocScale | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of RNA import into nucleus / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA modification / 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) / 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 ...positive regulation of RNA import into nucleus / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA modification / 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) / 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 / rRNA methylation / GDP-dissociation inhibitor activity / : / U3 snoRNA binding / poly(A)+ mRNA export from nucleus / 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 / snoRNA binding / 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 / 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 / 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 / unfolded protein binding / ribosome binding / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / phosphorylation / negative regulation of gene expression / protein serine kinase activity / mRNA binding / GTPase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / 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 S288c (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Shayan R / Mitterer V / Ferreira-Cerca S / Murat G / Enne T / Rinaldi D / Weigl S / Omanic H / Gleizes PE / Kressler D ...Shayan R / Mitterer V / Ferreira-Cerca S / Murat G / Enne T / Rinaldi D / Weigl S / Omanic H / Gleizes PE / Kressler D / Pertschy B / Plisson-Chastang C | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism. Authors: Valentin Mitterer / Ramtin Shayan / Sébastien Ferreira-Cerca / Guillaume Murat / Tanja Enne / Dana Rinaldi / Sarah Weigl / Hajrija Omanic / Pierre-Emmanuel Gleizes / Dieter Kressler / Celia ...Authors: Valentin Mitterer / Ramtin Shayan / Sébastien Ferreira-Cerca / Guillaume Murat / Tanja Enne / Dana Rinaldi / Sarah Weigl / Hajrija Omanic / Pierre-Emmanuel Gleizes / Dieter Kressler / Celia Plisson-Chastang / Brigitte Pertschy / Abstract: Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is ...Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-EM, we show that ribosomal protein Rps20 orchestrates communication between two multi-step maturation events across the pre-40S subunit. Our study reveals that during pre-40S maturation, formation of essential contacts between Rps20 and Rps3 permits assembly factor Ltv1 to recruit the Hrr25 kinase, thereby promoting Ltv1 phosphorylation. In parallel, a deeply buried Rps20 loop reaches to the opposite pre-40S side, where it stimulates Rio2 ATPase activity. Both cascades converge to the final maturation steps releasing Rio2 and phosphorylated Ltv1. We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps. | |||||||||
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_4793.map.gz | 21.6 MB | EMDB map data format | |
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Header (meta data) | emd-4793-v30.xml emd-4793.xml | 52.1 KB 52.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4793_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_4793.png | 188.8 KB | ||
Others | emd_4793_half_map_1.map.gz emd_4793_half_map_2.map.gz | 171.4 MB 171.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4793 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4793 | 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_4793.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Yeast pre-40S particle, purified using Tsr1-TAP as bait, in mutant conditions (deletion of aa 68-78 of Rps20) Structural class 2 Final EM map; local sharpening with LocScale | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Yeast pre-40S particle, purified using Tsr1-TAP as bait,...
File | emd_4793_half_map_1.map | ||||||||||||
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Annotation | Yeast pre-40S particle, purified using Tsr1-TAP as bait, in mutant conditions (deletion of aa 68-78 of Rps20) Structural class 2 Unfiltered half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Yeast pre-40S particle, purified using Tsr1-TAP as bait,...
File | emd_4793_half_map_2.map | ||||||||||||
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Annotation | Yeast pre-40S particle, purified using Tsr1-TAP as bait, in mutant conditions (deletion of aa 68-78 of Rps20) Structural class 2 Unfiltered half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : C2-S20DeltaLoop State 2 of yeast pre-40S particles purified with ...
+Supramolecule #1: C2-S20DeltaLoop State 2 of yeast pre-40S particles purified with ...
+Macromolecule #1: 18S 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 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 S11-A
+Macromolecule #11: 40S ribosomal protein S13
+Macromolecule #12: 40S ribosomal protein S14-A
+Macromolecule #13: 40S ribosomal protein S17-A
+Macromolecule #14: 40S ribosomal protein S21-A
+Macromolecule #15: 40S ribosomal protein S22-A
+Macromolecule #16: 40S ribosomal protein S23-A
+Macromolecule #17: 40S ribosomal protein S24-A
+Macromolecule #18: 40S ribosomal protein S27-A
+Macromolecule #19: 40S ribosomal protein S29-A
+Macromolecule #20: 40S ribosomal protein S30-A
+Macromolecule #21: 40S ribosomal protein S3
+Macromolecule #22: 40S ribosomal protein S5
+Macromolecule #23: 40S ribosomal protein S10-A
+Macromolecule #24: 40S ribosomal protein S12
+Macromolecule #25: 40S ribosomal protein S15
+Macromolecule #26: 40S ribosomal protein S16-A
+Macromolecule #27: 40S ribosomal protein S18-A
+Macromolecule #28: 40S ribosomal protein S19-A
+Macromolecule #29: 40S ribosomal protein S20
+Macromolecule #30: 40S ribosomal protein S25-A
+Macromolecule #31: 40S ribosomal protein S28-A
+Macromolecule #32: Ubiquitin-40S ribosomal protein S31
+Macromolecule #33: Guanine nucleotide-binding protein subunit beta-like protein
-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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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.045 kPa / Details: 25 mA, 30sec |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: blot 1.7-1.9 seconds before plunging. |
-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 / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm |
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) / Detector mode: COUNTING / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 6480 / Average electron dose: 32.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |