- EMDB-4793: State 2 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles -
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Basic information
Entry
Database: EMDB / ID: EMD-4793
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
Complex: 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)
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 modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (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 modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (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 / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / ribosome-associated ubiquitin-dependent protein catabolic process / 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 / poly(A)+ mRNA export from nucleus / 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 / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / positive regulation of protein kinase activity / regulation of translational fidelity / Ub-specific processing proteases / ribosomal small subunit export from nucleus / translation regulator activity / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / 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 / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / unfolded protein binding / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / protein ubiquitination / structural constituent of ribosome / translation / phosphorylation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
Serine/threonine-protein kinase Rio2 / RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase / RIO-like kinase / RIO1 family / Ribosomal RNA adenine dimethylase / Krr1, KH1 domain / Krr1 KH1 domain / Bystin ...Serine/threonine-protein kinase Rio2 / RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase / RIO-like kinase / RIO1 family / Ribosomal RNA adenine dimethylase / Krr1, KH1 domain / Krr1 KH1 domain / Bystin / Bystin / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / K Homology domain, type 1 superfamily / : / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 Similarity search - Domain/homology
Small ribosomal subunit protein uS4A / Small ribosomal subunit protein eS17A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A ...Small ribosomal subunit protein uS4A / Small ribosomal subunit protein eS17A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Small ribosomal subunit protein RACK1 / Essential nuclear protein 1 / Small ribosomal subunit protein uS10 / Serine/threonine-protein kinase RIO2 / Small ribosomal subunit protein uS14A / Dimethyladenosine transferase / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS19 / Ribosome biogenesis protein TSR1 / Small ribosomal subunit protein eS10A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A / Pre-rRNA-processing protein PNO1 Similarity search - Component
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
Deposition
Apr 10, 2019
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Header (metadata) release
May 1, 2019
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Map release
Jun 26, 2019
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Update
May 22, 2024
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Current status
May 22, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_4793.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour Level
By AUTHOR: 0.095 / Movie #1: 0.095
Minimum - Maximum
-0.22846869 - 0.5547447
Average (Standard dev.)
0.002889833 (±0.019886581)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
384
384
384
Spacing
384
384
384
Cell
A=B=C: 409.72803 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.067
1.067
1.067
M x/y/z
384
384
384
origin x/y/z
0.000
0.000
0.000
length x/y/z
409.728
409.728
409.728
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
384
384
384
D min/max/mean
-0.228
0.555
0.003
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Supplemental data
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Half map: Yeast pre-40S particle, purified using Tsr1-TAP as bait,...
Entire : C2-S20DeltaLoop State 2 of yeast pre-40S particles purified with ...
Entire
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)
Components
Complex: 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)
RNA: 18S ribosomal RNA
Protein or peptide: 40S ribosomal protein S0-A
Protein or peptide: 40S ribosomal protein S1-A
Protein or peptide: 40S ribosomal protein S2
Protein or peptide: 40S ribosomal protein S4-A
Protein or peptide: 40S ribosomal protein S6-A
Protein or peptide: 40S ribosomal protein S7-A
Protein or peptide: 40S ribosomal protein S8-A
Protein or peptide: 40S ribosomal protein S9-A
Protein or peptide: 40S ribosomal protein S11-A
Protein or peptide: 40S ribosomal protein S13
Protein or peptide: 40S ribosomal protein S14-A
Protein or peptide: 40S ribosomal protein S17-A
Protein or peptide: 40S ribosomal protein S21-A
Protein or peptide: 40S ribosomal protein S22-A
Protein or peptide: 40S ribosomal protein S23-A
Protein or peptide: 40S ribosomal protein S24-A
Protein or peptide: 40S ribosomal protein S27-A
Protein or peptide: 40S ribosomal protein S29-A
Protein or peptide: 40S ribosomal protein S30-A
Protein or peptide: 40S ribosomal protein S3
Protein or peptide: 40S ribosomal protein S5
Protein or peptide: 40S ribosomal protein S10-A
Protein or peptide: 40S ribosomal protein S12
Protein or peptide: 40S ribosomal protein S15
Protein or peptide: 40S ribosomal protein S16-A
Protein or peptide: 40S ribosomal protein S18-A
Protein or peptide: 40S ribosomal protein S19-A
Protein or peptide: 40S ribosomal protein S20
Protein or peptide: 40S ribosomal protein S25-A
Protein or peptide: 40S ribosomal protein S28-A
Protein or peptide: Ubiquitin-40S ribosomal protein S31
Protein or peptide: Guanine nucleotide-binding protein subunit beta-like protein
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Supramolecule #1: C2-S20DeltaLoop State 2 of yeast pre-40S particles purified with ...
Supramolecule
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: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)
Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weight
Theoretical: 1.2 MDa
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Macromolecule #1: 18S ribosomal RNA
Macromolecule
Name: 18S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / 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.
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Electron microscopy
Microscope
FEI TITAN KRIOS
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
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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