[English] 日本語
Yorodumi- EMDB-0953: Cryo-EM structure of 90S small subunit preribosomes in transition... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0953 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of 90S small subunit preribosomes in transition states (State E) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / RIBOSOME | |||||||||
Function / homology | Function and homology information box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / nuclear microtubule / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / nuclear microtubule / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA binding / snRNA binding / tRNA re-export from nucleus / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / regulation of transcription by RNA polymerase I / box C/D sno(s)RNA 3'-end processing / rDNA heterochromatin / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of rRNA processing / single-stranded telomeric DNA binding / U4/U6 snRNP / tRNA export from nucleus / 90S preribosome assembly / rRNA base methylation / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / SUMOylation of RNA binding proteins / O-methyltransferase activity / protein localization to nucleolus / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / poly(U) RNA binding / U4 snRNP / 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 / preribosome, small subunit precursor / establishment of cell polarity / snoRNA binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / 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 / 90S preribosome / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / RNA processing / 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) / U4/U6 x U5 tri-snRNP complex / enzyme activator activity / RNA endonuclease activity / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / spliceosomal complex / maintenance of translational fidelity / mRNA splicing, via spliceosome / rRNA processing / ribosome biogenesis / peroxisome / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA 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
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
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 | |
---|---|---|---|---|
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 |
-Validation report
Summary document | emd_0953_validation.pdf.gz | 411 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0953_full_validation.pdf.gz | 410.5 KB | Display | |
Data in XML | emd_0953_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | emd_0953_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0953 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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 |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| |||||||||
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 |
---|---|
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |