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- EMDB-0955: 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-0955 | |||||||||
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Title | Cryo-EM structure of 90S small subunit preribosomes in transition states (State C1) | |||||||||
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![]() | ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / RIBOSOME | |||||||||
Function / homology | ![]() mRNA modification / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / tRNA wobble cytosine modification / rRNA 2'-O-methylation ...mRNA modification / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / tRNA wobble cytosine modification / rRNA 2'-O-methylation / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / nuclear microtubule / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / snRNA binding / positive regulation of RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / 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) / regulation of transcription by RNA polymerase I / positive regulation of rRNA processing / U4/U6 snRNP / single-stranded telomeric DNA binding / rRNA primary transcript binding / rRNA base methylation / O-methyltransferase activity / small nuclear ribonucleoprotein complex / SUMOylation of RNA binding proteins / sno(s)RNA-containing ribonucleoprotein complex / protein localization to nucleolus / U4 snRNA binding / box C/D methylation guide snoRNP complex / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / U4 snRNP / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / U3 snoRNA binding / 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 / establishment of cell polarity / snoRNA binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / 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 / regulation of translational fidelity / RNA processing / ribosomal subunit export from nucleus / Cajal body / 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) / vesicle-mediated transport / U4/U6 x U5 tri-snRNP complex / enzyme activator activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / protein transport / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / cell cycle / GTPase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
![]() | 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 | ![]() | 16.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 97.2 KB 97.2 KB | Display Display | ![]() |
Images | ![]() | 68.8 KB | ||
Filedesc metadata | ![]() | 26.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 412.8 KB | Display | ![]() |
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Full document | ![]() | 412.4 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lqvMC ![]() 0949C ![]() 0950C ![]() 0951C ![]() 0952C ![]() 0953C ![]() 0954C ![]() 6lqpC ![]() 6lqqC ![]() 6lqrC ![]() 6lqsC ![]() 6lqtC ![]() 6lquC 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 C1)
+Supramolecule #1: 90S pre-ribosome (Dhr1-depleted, state C1)
+Macromolecule #1: U3 snoRNA
+Macromolecule #2: 5' ETS
+Macromolecule #3: 18S pre-rRNA
+Macromolecule #4: 40S ribosomal protein S4-A
+Macromolecule #5: 40S ribosomal protein S5
+Macromolecule #6: 40S ribosomal protein S6-A
+Macromolecule #7: 40S ribosomal protein S8-A
+Macromolecule #8: 40S ribosomal protein S9-A
+Macromolecule #9: 40S ribosomal protein S11-A
+Macromolecule #10: 40S ribosomal protein S16-A
+Macromolecule #11: 40S ribosomal protein S23-A
+Macromolecule #12: 40S ribosomal protein S24-A
+Macromolecule #13: 40S ribosomal protein S28-A
+Macromolecule #14: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #15: Nucleolar protein 56
+Macromolecule #16: Nucleolar protein 58
+Macromolecule #17: Ribosomal RNA-processing protein 9
+Macromolecule #18: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #19: U3 small nucleolar RNA-associated protein 4
+Macromolecule #20: U3 small nucleolar RNA-associated protein 5
+Macromolecule #21: U3 small nucleolar RNA-associated protein 8
+Macromolecule #22: U3 small nucleolar RNA-associated protein 9
+Macromolecule #23: U3 small nucleolar RNA-associated protein 10
+Macromolecule #24: U3 small nucleolar RNA-associated protein 15
+Macromolecule #25: NET1-associated nuclear protein 1
+Macromolecule #26: Periodic tryptophan protein 2
+Macromolecule #27: U3 small nucleolar RNA-associated protein 12
+Macromolecule #28: U3 small nucleolar RNA-associated protein 13
+Macromolecule #29: U3 small nucleolar RNA-associated protein 18
+Macromolecule #30: U3 small nucleolar RNA-associated protein 21
+Macromolecule #31: U3 small nucleolar RNA-associated protein 6
+Macromolecule #32: Bud site selection protein 21
+Macromolecule #33: U3 small nucleolar RNA-associated protein 7
+Macromolecule #34: U3 small nucleolar RNA-associated protein 11
+Macromolecule #35: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #36: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #37: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #38: Something about silencing protein 10
+Macromolecule #39: Protein SOF1
+Macromolecule #40: rRNA-processing protein FCF2
+Macromolecule #41: rRNA-processing protein FCF1
+Macromolecule #42: Ribosome biogenesis protein ENP2
+Macromolecule #43: U3 small nucleolar ribonucleoprotein protein LCP5
+Macromolecule #44: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #45: Ribosome biogenesis protein BMS1
+Macromolecule #46: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #47: RNA cytidine acetyltransferase
+Macromolecule #48: Nucleolar complex protein 14
+Macromolecule #49: Nucleolar complex protein 4
+Macromolecule #50: U3 small nucleolar RNA-associated protein 20
+Macromolecule #51: U3 small nucleolar RNA-associated protein 14
+Macromolecule #52: Essential nuclear protein 1
+Macromolecule #53: Protein BFR2
+Macromolecule #54: Unassigned helices
+Macromolecule #55: ZINC ION
+Macromolecule #56: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #57: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | 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: Quantifoil R1.2/1.3 / 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: ![]() |
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 |