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Yorodumi- PDB-5fcj: Structure of the anisomycin-containing uL3 W255C mutant 80S yeast... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5fcj | |||||||||||||||||||||
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| Title | Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome | |||||||||||||||||||||
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Keywords | RIBOSOME / uL3 mutant / Anisomycin | |||||||||||||||||||||
| Function / homology | Function and homology informationtriplex DNA binding / Platelet degranulation / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / : ...triplex DNA binding / Platelet degranulation / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / : / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / telomeric DNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / positive regulation of protein kinase activity / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / TOR signaling / negative regulation of translational frameshifting / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / G-protein alpha-subunit binding / ribosomal large subunit export from nucleus / 90S preribosome / Ub-specific processing proteases / translational termination / regulation of translational fidelity / ribosomal subunit export from nucleus / protein-RNA complex assembly / maturation of LSU-rRNA / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation repressor activity / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled cytosolic ribosome / telomere maintenance / cellular response to amino acid starvation / protein kinase C binding / ribosomal large subunit biogenesis / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / mitochondrion / DNA binding Similarity search - Function | |||||||||||||||||||||
| Biological species | ![]() | |||||||||||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||||||||||||||
Authors | Mailliot, J. / Garreau de Loubresse, N. / Yusupova, G. / Dinman, J.D. / Yusupov, M. | |||||||||||||||||||||
| Funding support | France, Russian Federation, United States, 6items
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Citation | Journal: J.Mol.Biol. / Year: 2016Title: Crystal Structures of the uL3 Mutant Ribosome: Illustration of the Importance of Ribosomal Proteins for Translation Efficiency. Authors: Mailliot, J. / Garreau de Loubresse, N. / Yusupova, G. / Meskauskas, A. / Dinman, J.D. / Yusupov, M. | |||||||||||||||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5fcj.cif.gz | 9.9 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb5fcj.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 5fcj.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/5fcj ftp://data.pdbj.org/pub/pdb/validation_reports/fc/5fcj | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 5fciC ![]() 4v88S S: Starting model for refinement 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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| 2 | ![]()
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| Unit cell |
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Components
-RNA chain , 4 types, 8 molecules 26153748
| #1: RNA chain | Mass: 579761.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #36: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #37: RNA chain | Mass: 38951.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #38: RNA chain | Mass: 50682.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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+40S ribosomal protein ... , 31 types, 62 molecules S0s0S1s1S2s2S3s3S4s4S5s5S6s6S7s7S8s8S9s9C0c0C1c1C2c2C3c3C4c4...
-Protein , 5 types, 9 molecules E1e1SRsRSMsMQ0q0p0
| #33: Protein | Mass: 8703.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #34: Protein | Mass: 34710.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #35: Protein | Mass: 18715.916 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Remaining misalignments result from differences in the distribution of (UNK)s between the two instances of the molecule in the structure. Here is the original sequence ot the crystallized protein : MSNPFDLLGNDVEDADVVVLPPKEIVKSNTSSKKADVPPPSADPSKARKNRPRPSGNEGAIRDKTAGRRNNRSKDVTDSA TTKKSNTRRATDRHSRTGKTDTKKKVNQGWGDDKKELSAEKEAQADAAAEIAEDAAEAEDAGKPKTAQLSLQDYLNQQAN NQFNKVPEAKKVELDAERIETAEKEAYVPATKVKNVKSKQLKTKEYLEFDATFVESNTRKNFGDRNNNSRNNFNNRRGGR GARKGNNTANATNSANTVQKNRNIDVSNLPSLA Source: (natural) ![]() #76: Protein | Mass: 6032.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #81: Protein | | Mass: 33617.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. ...Details: (UNK) residues correspond to residues that aren't well resolved, and for which side-chains could not be modeled. (UNK)s were substituted in the original sequence of the crystallized protein. Here is the original sequence ot the crystallized protein : GGIREKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKLLPFVK GNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRAVNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDA GNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQVFPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLIN NYKDLLAVAIAASYHYPEIEDLVDRIENPEKYAAAAPAATSAASGDAAPAEEAAAEEEEESDDDMGFGLFD Source: (natural) ![]() |
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+60S ribosomal protein ... , 43 types, 83 molecules L2l2L3l3L4l4L5l5L6l6L7l7L8l8L9l9M0m0M1m1M3m3M4m4M5m5M6m6M7m7...
-Non-polymers , 4 types, 2030 molecules 






| #84: Chemical | ChemComp-MG / #85: Chemical | ChemComp-OHX / #86: Chemical | ChemComp-ZN / #87: Chemical | ChemComp-ANM / | |
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-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.96 % |
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| Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: Tris-Acetate pH7.0, KSCN, Mg-Acetate, Glycerol, Spermidine, PEG20000 |
-Data collection
| Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.15873 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Radiation wavelength | Wavelength: 1.15873 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection | Resolution: 3.1→49.958 Å / Num. obs: 1333169 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 76.76 Å2 / Rmerge F obs: 0.986 / Rmerge(I) obs: 0.389 / Rrim(I) all: 0.407 / Χ2: 0.938 / Net I/σ(I): 6.77 / Num. measured all: 12034750 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 4V88 Resolution: 3.1→49.958 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.89 / Stereochemistry target values: ML
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| Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso max: 493.66 Å2 / Biso mean: 70.2526 Å2 / Biso min: 20.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: final / Resolution: 3.1→49.958 Å
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| Refine LS restraints |
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| LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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X-RAY DIFFRACTION
France,
Russian Federation,
United States, 6items
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