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- PDB-6lqs: Cryo-EM structure of 90S small subunit preribosomes in transition... -
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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) | |||||||||
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![]() | RIBOSOME / ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 | |||||||||
Function / homology | ![]() nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / regulation of ribosomal protein gene transcription by RNA polymerase II / U1 snRNA 3'-end processing / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / box H/ACA snoRNA binding / nuclear polyadenylation-dependent CUT catabolic process / RNA fragment catabolic process / U5 snRNA 3'-end processing / rRNA 2'-O-methylation / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / CURI complex / UTP-C complex / CUT catabolic process / U4 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear microtubule / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / nuclear exosome (RNase complex) / rRNA (pseudouridine) methyltransferase activity / nuclear-transcribed mRNA catabolic process, non-stop decay / rRNA modification / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / 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 / regulation of rRNA processing / septum digestion after cytokinesis / histone H2AQ104 methyltransferase activity / tRNA re-export from nucleus / snRNA binding / histone mRNA catabolic process / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 3'-5' RNA helicase activity / rRNA methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / rRNA catabolic process / 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 / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / poly(A) binding / rRNA primary transcript binding / mRNA 3'-UTR AU-rich region binding / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / SUMOylation of RNA binding proteins / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / 90S preribosome assembly / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mTORC1-mediated signalling / rRNA methylation / Protein hydroxylation / RNA catabolic process / U4 snRNP / regulation of telomere maintenance / U3 snoRNA binding / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / precatalytic spliceosome / Ribosomal scanning and start codon recognition / snoRNA binding / preribosome, small subunit precursor / maturation of 5.8S rRNA / nonfunctional rRNA decay / establishment of cell polarity / Major pathway of rRNA processing in the nucleolus and cytosol / rRNA metabolic process / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 5.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 653.8 KB | Display | |
Data in CIF | ![]() | 1.1 MB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 |
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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: ![]() ![]() | |||||||||||||||
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 |
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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: ![]() |
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 |
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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 |