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Yorodumi- PDB-6oig: Subunit joining exposes nascent pre-40S rRNA for processing and q... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oig | ||||||||||||
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Title | Subunit joining exposes nascent pre-40S rRNA for processing and quality control | ||||||||||||
Components |
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Keywords | RIBOSOME / 80S-like complex / 60S | ||||||||||||
Function / homology | Function and homology information hexon binding / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome ...hexon binding / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / regulation of translational fidelity / protein-RNA complex assembly / translational termination / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / host cell nucleus / nucleolus / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Rai, J. / Parker, M.D. / Ghalei, H. / Johnson, M.C. / Karbstein, K. / Stroupe, M.E. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: RNA / Year: 2021 Title: An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7. Authors: Jay Rai / Melissa D Parker / Haina Huang / Stefan Choy / Homa Ghalei / Matthew C Johnson / Katrin Karbstein / M Elizabeth Stroupe / Abstract: During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly ...During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly intermediates are essential for maturation and quality control, how they form, and how their structure promotes quality control, remains unknown. To address these questions, we determined the structure of an 80S-like ribosome assembly intermediate to an overall resolution of 3.4 Å. The structure, validated by biochemical data, resolves a large body of previously paradoxical data and illustrates how assembly and translation factors cooperate to promote the formation of an interface that lacks many mature subunit contacts but is stabilized by the universally conserved methyltransferase Dim1. We also show how Tsr1 enables this interface by blocking the canonical binding of eIF5B to 40S subunits, while maintaining its binding to 60S. The structure also shows how this interface leads to unfolding of the platform, which allows for temporal regulation of the ATPase Fap7, thus linking 40S maturation to quality control during ribosome assembly. | ||||||||||||
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 | 6oig.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6oig.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6oig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oig_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6oig_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6oig_validation.xml.gz | 228.5 KB | Display | |
Data in CIF | 6oig_validation.cif.gz | 390.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oig ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oig | HTTPS FTP |
-Related structure data
Related structure data | 20077MC 6wdrC 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
+60S ribosomal protein ... , 41 types, 41 molecules zABCDEFGHIJsLMNOPQRSTUVWXYZabc...
-Protein , 2 types, 2 molecules mq
#40: Protein | Mass: 6032.321 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPL40A, UBI1, YIL148W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08 |
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#43: Protein | Mass: 23585.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPP0, L10E, RPA0, RPL10E, RPLA0, YLR340W, L8300.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317 |
-RNA chain , 3 types, 3 molecules 587
#44: RNA chain | Mass: 1096842.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) |
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#45: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1267176496 |
#46: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039024045 |
-Protein/peptide , 2 types, 2 molecules xy
#47: Protein/peptide | Mass: 4017.944 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) |
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#48: Protein/peptide | Mass: 3932.839 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) |
-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: 60S subunit of 80S-like ribosome / Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83558 / Symmetry type: POINT |