+Open data
-Basic information
Entry | Database: PDB / ID: 6rbe | ||||||
---|---|---|---|---|---|---|---|
Title | State 2 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles | ||||||
Components |
| ||||||
Keywords | RIBOSOME / pre-40S / yeast / cytoplasmic / mutant Rps20 | ||||||
Function / homology | Function and homology information 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 / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...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 / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / 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 / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / G-protein alpha-subunit binding / 90S preribosome / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ub-specific processing proteases / regulation of translational fidelity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / 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, P.E. / Kressler, D. ...Shayan, R. / Mitterer, V. / Ferreira-Cerca, S. / Murat, G. / Enne, T. / Rinaldi, D. / Weigl, S. / Omanic, H. / Gleizes, P.E. / Kressler, D. / Pertschy, B. / Plisson-Chastang, C. | ||||||
Funding support | France, 1items
| ||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6rbe.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rbe.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6rbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rbe_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6rbe_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6rbe_validation.xml.gz | 153.4 KB | Display | |
Data in CIF | 6rbe_validation.cif.gz | 252.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/6rbe ftp://data.pdbj.org/pub/pdb/validation_reports/rb/6rbe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 1 types, 1 molecules 2
#1: RNA chain | Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 1262303 |
---|
+40S ribosomal protein ... , 30 types, 30 molecules ABCEGHIJLNORVWXYbdeDFKMPQSTUZc
-Protein , 2 types, 2 molecules fg
#32: Protein | Mass: 17254.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P05759 |
---|---|
#33: Protein | Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P38011 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: C2-S20DeltaLoop State 2 of yeast pre-40S particles purified with Tsr1-TAP as bait, in mutant conditions (deletion of aa 68-78 of Rps20) Type: RIBOSOME / Entity ID: all / Source: NATURAL |
---|---|
Molecular weight | Value: 1.2 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 25 mA, 30sec / Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K / Details: blot 1.7-1.9 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 32.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6480 |
Image scans | Movie frames/image: 25 / Used frames/image: 1-25 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 645109 | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42901 / Algorithm: EXACT BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|