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Yorodumi- PDB-5fcj: Structure of the anisomycin-containing uL3 W255C mutant 80S yeast... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fcj | |||||||||||||||||||||
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Title | Structure of the anisomycin-containing uL3 W255C mutant 80S yeast ribosome | |||||||||||||||||||||
Components |
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Keywords | RIBOSOME / uL3 mutant / Anisomycin | |||||||||||||||||||||
Function / homology | Function and homology information triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / 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 / response to cycloheximide / telomeric DNA binding / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / translational termination / translation repressor activity / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / telomere maintenance / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / 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 | Saccharomyces cerevisiae S288c (yeast) | |||||||||||||||||||||
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: 2016 Title: 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: MolmilJmol/JSmol |
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-Downloads & links
-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
Summary document | 5fcj_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5fcj_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 5fcj_validation.xml.gz | 945.3 KB | Display | |
Data in CIF | 5fcj_validation.cif.gz | 1.4 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/5fcj ftp://data.pdbj.org/pub/pdb/validation_reports/fc/5fcj | HTTPS FTP |
-Related structure data
Related structure data | 5fciC 4v88S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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) Saccharomyces cerevisiae S288c (yeast) / References: REF: 831416132 #36: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: REF: 831416132 #37: RNA chain | Mass: 38951.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 834774822 #38: RNA chain | Mass: 50682.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: 940534893 |
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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) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05759 #34: Protein | Mass: 34710.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P38011 #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) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P39015 #76: Protein | Mass: 6032.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P0CH08 #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) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P05317 |
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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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-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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting 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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