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Yorodumi- PDB-6lqv: Cryo-EM structure of 90S small subunit preribosomes in transition... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lqv | |||||||||
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Title | Cryo-EM structure of 90S small subunit preribosomes in transition states (State C1) | |||||||||
Components |
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Keywords | RIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 | |||||||||
Function / homology | Function and homology information mRNA modification / Noc4p-Nop14p complex / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity ...mRNA modification / Noc4p-Nop14p complex / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / RNA fragment catabolic process / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / nuclear microtubule / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of RNA binding / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA export from nucleus / rRNA methyltransferase activity / regulation of transcription by RNA polymerase I / positive regulation of rRNA processing / single-stranded telomeric DNA binding / U4/U6 snRNP / rRNA base methylation / rRNA primary transcript binding / SUMOylation of RNA binding proteins / small nuclear ribonucleoprotein complex / O-methyltransferase activity / 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 / 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 / poly(A)+ mRNA export from nucleus / establishment of cell polarity / snoRNA binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / 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) / ribosomal subunit export from nucleus / RNA processing / enzyme activator activity / 90S preribosome / vesicle-mediated transport / U4/U6 x U5 tri-snRNP complex / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / protein transport / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / cell cycle / GTPase activity / mRNA binding / nucleolus / GTP binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Du, Y. / Ye, K. | |||||||||
Funding support | China, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lqv.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6lqv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6lqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/6lqv ftp://data.pdbj.org/pub/pdb/validation_reports/lq/6lqv | HTTPS FTP |
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-Related structure data
Related structure data | 0955MC 0949C 0950C 0951C 0952C 0953C 0954C 6lqpC 6lqqC 6lqrC 6lqsC 6lqtC 6lquC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+RNA chain , 3 types, 3 molecules 3A5ASA
+40S ribosomal protein ... , 10 types, 10 molecules SFSGSHSJSKSMSRSYSZSd
+Protein , 14 types, 18 molecules 3B3C3F3G3HAGB15B5H5IRGRHRKRLRMRSRYX1
+Nucleolar protein ... , 2 types, 2 molecules 3D3E
+U3 small nucleolar RNA-associated protein ... , 16 types, 16 molecules A4A5A8A9AEAFB2B3B8BEB65C5D5ERPRQ
+U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules 5F5GRB
+RRNA-processing protein ... , 2 types, 2 molecules 5J5K
+Ribosome biogenesis protein ... , 2 types, 2 molecules RARJ
+Nucleolar complex protein ... , 2 types, 2 molecules RNRO
+Non-polymers , 3 types, 3 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 90S pre-ribosome (Dhr1-depleted, state C1) / Type: COMPLEX / Entity ID: #1-#54 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 5 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c | |||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 10 / Num. of real images: 18028 |
Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 382298 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9421 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6LQR Accession code: 6LQR / Source name: PDB / Type: experimental model |