+Open data
-Basic information
Entry | Database: PDB / ID: 6qt0 | |||||||||
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Title | Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles | |||||||||
Components |
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Keywords | RIBOSOME / 60S subunit / eIF6 / Nmd3 / Lsg1 | |||||||||
Function / homology | Function and homology information maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / 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 / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / 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 / ribosomal large subunit binding / 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 / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / translational termination / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / 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: 3.4 Å | |||||||||
Authors | Kargas, V. / Warren, A.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Elife / Year: 2019 Title: Mechanism of completion of peptidyltransferase centre assembly in eukaryotes. Authors: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / ...Authors: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / Leszek Wawiórka / Stefan Mv Freund / Jane L Wagstaff / Antonina Andreeva / Alexandre Faille / Edwin Chen / Florian Stengel / Helmut Bergler / Alan John Warren / Abstract: During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase ...During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies. | |||||||||
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 | 6qt0.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6qt0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6qt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qt0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6qt0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6qt0_validation.xml.gz | 190.9 KB | Display | |
Data in CIF | 6qt0_validation.cif.gz | 334.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/6qt0 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/6qt0 | HTTPS FTP |
-Related structure data
Related structure data | 4630MC 4560C 4636C 4884C 6qikC 6qtzC 6ri5C 6rzzC 6s05C 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 Axy
#1: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822 |
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#44: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1329886537 |
#45: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1331532632 |
+60S ribosomal protein ... , 39 types, 39 molecules BCDEFGHqJKLMNOPQRSTUVWXYZabcde...
-Protein , 3 types, 3 molecules ntz
#40: Protein | Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q12522 |
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#41: Protein | Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / References: UniProt: P0CH08 |
#43: Protein | Mass: 49763.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae / References: UniProt: Q06709 |
-Non-polymers , 1 types, 5 molecules
#46: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-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: Lsg1-TAP 60s ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#45 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: 63 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46734 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4V88 Accession code: 4V88 / Source name: PDB / Type: experimental model |