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Yorodumi- PDB-6lqs: Cryo-EM structure of 90S small subunit preribosomes in transition... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lqs | |||||||||
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Title | Cryo-EM structure of 90S small subunit preribosomes in transition states (State D) | |||||||||
Components |
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Keywords | RIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 | |||||||||
Function / homology | Function and homology information nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / nuclear polyadenylation-dependent mRNA catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / U1 snRNA 3'-end processing / Noc4p-Nop14p complex / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / rRNA 2'-O-methylation / U5 snRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / CURI complex / UTP-C complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / U4 snRNA 3'-end processing / 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 / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / nuclear-transcribed mRNA catabolic process, non-stop decay / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / 3'-5' RNA helicase activity / histone mRNA catabolic process / nuclear mRNA surveillance / 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 catabolic process / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / positive regulation of rRNA processing / single-stranded telomeric DNA binding / U4/U6 snRNP / tRNA export from nucleus / mRNA 3'-UTR AU-rich region binding / 90S preribosome assembly / poly(A) binding / 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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / mTORC1-mediated signalling / Protein hydroxylation / RNA catabolic process / rRNA methylation / poly(U) RNA binding / U4 snRNP / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / regulation of telomere maintenance / 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 / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / establishment of cell polarity / snoRNA binding / precatalytic spliceosome / rRNA metabolic process / maturation of 5.8S rRNA / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 | 6lqs.cif.gz | 5.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6lqs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6lqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lqs_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6lqs_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6lqs_validation.xml.gz | 653.8 KB | Display | |
Data in CIF | 6lqs_validation.cif.gz | 1.1 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/6lqs ftp://data.pdbj.org/pub/pdb/validation_reports/lq/6lqs | HTTPS FTP |
-Related structure data
Related structure data | 0952MC 0949C 0950C 0951C 0953C 0954C 0955C 6lqpC 6lqqC 6lqrC 6lqtC 6lquC 6lqvC 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 ... , 16 types, 16 molecules SCSFSGSHSISJSKSMSOSPSRSXSYSZScSd
+Protein , 17 types, 20 molecules 3B3C3G3HAGB15B5H5IRDRGRHRJRKRSRTRWR7M4M6
+Nucleolar protein ... , 2 types, 2 molecules 3D3E
+Ribosomal RNA-processing protein ... , 2 types, 2 molecules 3FRF
+U3 small nucleolar RNA-associated protein ... , 17 types, 17 molecules A4A5A8A9AEAFB2B3B8BEB65C5D5ERERPRQ
+U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules 5F5G
+RRNA-processing protein ... , 2 types, 2 molecules 5J5K
+Nucleolar complex protein ... , 2 types, 2 molecules RNRO
+Unassigned helices ... , 2 types, 2 molecules X1X2
+Exosome complex component ... , 9 types, 9 molecules R5R1R3R6R2M3R0r4C4
+Exosome complex exonuclease ... , 2 types, 2 molecules R4r6
+Non-polymers , 3 types, 4 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 D) / Type: COMPLEX / Entity ID: #1-#76 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 5 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||
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 FIELD / 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75404 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6LQP Accession code: 6LQP / Source name: PDB / Type: experimental model |