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- 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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Function / homology | ![]() Noc4p-Nop14p complex / box H/ACA snoRNA binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Du Y / Ye K | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 17.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 98.9 KB 98.9 KB | Display Display | ![]() |
Images | ![]() | 66.6 KB | ||
Filedesc metadata | ![]() | 26.7 KB | ||
Archive directory | ![]() ![]() | 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 | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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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
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
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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 |