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Yorodumi- EMDB-0953: Cryo-EM structure of 90S small subunit preribosomes in transition... -
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Open data
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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) | |||||||||
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Keywords | ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / RIBOSOME | |||||||||
| Function / homology | Function and homology informationregulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Noc4p-Nop14p complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex ...regulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Noc4p-Nop14p complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / snoRNA guided rRNA 2'-O-methylation / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / box C/D sno(s)RNA binding / rRNA modification / histone H2AQ104 methyltransferase activity / septum digestion after cytokinesis / regulation of rRNA processing / tRNA re-export from nucleus / snRNA binding / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / rDNA heterochromatin / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / U4 snRNA binding / O-methyltransferase activity / SUMOylation of RNA binding proteins / 90S preribosome assembly / protein localization to nucleolus / mTORC1-mediated signalling / rRNA methylation / Protein hydroxylation / U4 snRNP / 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 / Ribosomal scanning and start codon recognition / snoRNA binding / precatalytic spliceosome / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / establishment of cell polarity / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / Ub-specific processing proteases / ribosomal subunit export from nucleus / RNA processing / regulation of translational fidelity / 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 / RNA endonuclease activity / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / spliceosomal complex / small-subunit processome / translational initiation / enzyme activator activity / mRNA splicing, via spliceosome / maintenance of translational fidelity / rRNA processing / peroxisome / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation Similarity search - Function | |||||||||
| Biological species | ![]() ![]() | |||||||||
| 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: 2020Title: 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. | |||||||||
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Structure visualization
| Movie |
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
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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 |
-Validation report
| Summary document | emd_0953_validation.pdf.gz | 411 KB | Display | EMDB validaton report |
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| 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 ( M: atomic model generated by this map |
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| Similar structure data |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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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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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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
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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 |
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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 |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| 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 |
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About Yorodumi


Keywords
Authors
China, 2 items
Citation
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