+Open data
-Basic information
Entry | Database: PDB / ID: 8p8m | ||||||
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Title | Yeast 60S ribosomal subunit, RPL39 deletion | ||||||
Components |
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Keywords | RIBOSOME / 60S ribosomal subunit / protein exit tunnel / RPL39 | ||||||
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: 2.66 Å | ||||||
Authors | Rabl, J. / Banerjee, A. / Boehringer, D. / Zavolan, M. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Yeast 60S ribosomal subunit, RPL39 deletion Authors: Rabl, J. / Banerjee, A. / Boehringer, D. / Zavolan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p8m.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8p8m.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8p8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p8m_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8p8m_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8p8m_validation.xml.gz | 204.2 KB | Display | |
Data in CIF | 8p8m_validation.cif.gz | 339.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/8p8m ftp://data.pdbj.org/pub/pdb/validation_reports/p8/8p8m | HTTPS FTP |
-Related structure data
Related structure data | 17549MC 8p8nC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules ALDLE
#1: RNA chain | Mass: 1097470.750 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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#11: 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 |
#13: 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 |
+60S ribosomal protein ... , 38 types, 38 molecules QYJTQZJURAJVRBJWRCRDRELFRFLGRGLHRHLIRILJRJLKRMLLLMRQLNRTLOQO...
-Protein , 2 types, 2 molecules RORV
#28: Protein | Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0CH08 |
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#34: Protein | Mass: 33749.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317 |
-Non-polymers , 4 types, 163 molecules
#44: Chemical | ChemComp-MG / #45: Chemical | ChemComp-SPM / | #46: Chemical | ChemComp-SPD / | #47: 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: Yeast 60S ribosomal subunit without ribosomal protein RPL39 Type: RIBOSOME Entity ID: #1, #3, #5, #7, #9, #11, #13, #15, #17, #19, #21, #23, #25, #27, #29, #31, #33, #35-#43, #2, #4, #6, #8, #10, #12, #14, #16, #18, #20, #22, #24, #26, #28, #30, #32, #34 Source: NATURAL |
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Molecular weight | Value: 1.76 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: 1000 nm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41172 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.02 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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