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Yorodumi- EMDB-0953: Cryo-EM structure of 90S small subunit preribosomes in transition... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0953 | |||||||||
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Title | Cryo-EM structure of 90S small subunit preribosomes in transition states (State E) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / RIBOSOME | |||||||||
Function / homology | Function and homology information Noc4p-Nop14p complex / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome ...Noc4p-Nop14p complex / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / histone H2AQ104 methyltransferase activity / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA modification / septum digestion after cytokinesis / snRNA binding / positive regulation of RNA binding / SUMOylation of RNA binding proteins / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / regulation of transcription by RNA polymerase I / 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) / rDNA heterochromatin / rRNA methyltransferase activity / positive regulation of rRNA processing / box C/D methylation guide snoRNP complex / U4/U6 snRNP / rRNA base methylation / single-stranded telomeric DNA binding / rRNA primary transcript binding / 90S preribosome assembly / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / U4 snRNP / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / poly(U) RNA binding / 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 / precatalytic spliceosome / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / snoRNA binding / spliceosomal complex assembly / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / 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 / nucleolar large rRNA transcription by RNA polymerase I / 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 / enzyme activator 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) / regulation of translational fidelity / RNA processing / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / small-subunit processome / maintenance of translational fidelity / spliceosomal complex / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / mRNA splicing, via spliceosome / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / cell cycle / translation / mRNA binding / GTPase activity / GTP binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Du Y / Ye K | |||||||||
Funding support | China, 2 items
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Citation | Journal: Science / Year: 2020 Title: Cryo-EM structure of 90 small ribosomal subunit precursors in transition states. Authors: Yifei Du / Weidong An / Xing Zhu / Qi Sun / Jia Qi / Keqiong Ye / Abstract: The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by ...The 90 preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of intermediates in the path from the 90 to the pre-40 The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 progression. | |||||||||
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_0953.map.gz | 17.3 MB | EMDB map data format | |
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Header (meta data) | emd-0953-v30.xml emd-0953.xml | 98.9 KB 98.9 KB | Display Display | EMDB header |
Images | emd_0953.png | 66.6 KB | ||
Filedesc metadata | emd-0953.cif.gz | 26.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0953 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0953 | HTTPS FTP |
-Related structure data
Related structure data | 6lqtMC 0949C 0950C 0951C 0952C 0954C 0955C 6lqpC 6lqqC 6lqrC 6lqsC 6lquC 6lqvC C: citing same article (ref.) M: atomic model generated by this map |
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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_0953.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : 90S pre-ribosome (Dhr1-depleted, state E)
+Supramolecule #1: 90S pre-ribosome (Dhr1-depleted, state E)
+Macromolecule #1: U3 snoRNA
+Macromolecule #2: 5' ETS
+Macromolecule #3: 18S pre-rRNA
+Macromolecule #4: 40S ribosomal protein S1-A
+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 S13
+Macromolecule #13: 40S ribosomal protein S14-A
+Macromolecule #14: 40S ribosomal protein S16-A
+Macromolecule #15: 40S ribosomal protein S22-B
+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 S28-A
+Macromolecule #20: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #21: Nucleolar protein 56
+Macromolecule #22: Nucleolar protein 58
+Macromolecule #23: Ribosomal RNA-processing protein 9
+Macromolecule #24: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #25: U3 small nucleolar RNA-associated protein 4
+Macromolecule #26: U3 small nucleolar RNA-associated protein 5
+Macromolecule #27: U3 small nucleolar RNA-associated protein 9
+Macromolecule #28: U3 small nucleolar RNA-associated protein 10
+Macromolecule #29: U3 small nucleolar RNA-associated protein 15
+Macromolecule #30: NET1-associated nuclear protein 1
+Macromolecule #31: Periodic tryptophan protein 2
+Macromolecule #32: U3 small nucleolar RNA-associated protein 12
+Macromolecule #33: U3 small nucleolar RNA-associated protein 13
+Macromolecule #34: U3 small nucleolar RNA-associated protein 18
+Macromolecule #35: U3 small nucleolar RNA-associated protein 21
+Macromolecule #36: U3 small nucleolar RNA-associated protein 6
+Macromolecule #37: U3 small nucleolar RNA-associated protein 7
+Macromolecule #38: U3 small nucleolar RNA-associated protein 11
+Macromolecule #39: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #40: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #41: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #42: Something about silencing protein 10
+Macromolecule #43: Protein SOF1
+Macromolecule #44: rRNA-processing protein FCF2
+Macromolecule #45: rRNA-processing protein FCF1
+Macromolecule #46: rRNA biogenesis protein RRP5
+Macromolecule #47: U3 small nucleolar RNA-associated protein 22
+Macromolecule #48: Ribosomal RNA-processing protein 7
+Macromolecule #49: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #50: Ribosome biogenesis protein BMS1
+Macromolecule #51: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #52: Nucleolar complex protein 14
+Macromolecule #53: U3 small nucleolar RNA-associated protein 20
+Macromolecule #54: U3 small nucleolar RNA-associated protein 14
+Macromolecule #55: Pno1
+Macromolecule #56: Unassigned helices
+Macromolecule #57: ZINC ION
+Macromolecule #58: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #59: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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: 2.5 µm / Nominal defocus min: 1.5 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: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number grids imaged: 10 / Number real images: 18028 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 382298 |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION |
Final 3D classification | Number classes: 8 / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 14475 |