+Open data
-Basic information
Entry | Database: PDB / ID: 5fci | |||||||||||||||||||||
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Title | Structure of the vacant uL3 W255C mutant 80S yeast ribosome | |||||||||||||||||||||
Components |
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Keywords | RIBOSOME / uL3 mutant / Vacant | |||||||||||||||||||||
Function / homology | Function and homology information ribosome hibernation / triplex DNA binding / 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 / Protein methylation / RMTs methylate histone arginines ...ribosome hibernation / triplex DNA binding / 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 / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / : / 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / translational elongation / response to cycloheximide / telomeric DNA binding / mRNA destabilization / TOR signaling / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / protein-RNA complex assembly / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 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) / regulation of translational fidelity / positive regulation of protein kinase activity / rescue of stalled ribosome / translational termination / maturation of SSU-rRNA / translation repressor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / ribosome assembly / telomere maintenance / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 | 5fci.cif.gz | 10 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5fci.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5fci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/5fci ftp://data.pdbj.org/pub/pdb/validation_reports/fc/5fci | HTTPS FTP |
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-Related structure data
Related structure data | 5fcjC 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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1 |
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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) 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 ... , 33 types, 64 molecules S0s0S1s1S2s2S3s3S4s4S5s5S6s6S7s7S8s8S9s9C0C1c1C2c2C3c3C4c4C5...
-Protein , 4 types, 7 molecules SRsRSMsMQ0q0p0
#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 #82: Protein | | Mass: 33158.652 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 , 3 types, 2303 molecules
#85: Chemical | ChemComp-OHX / #86: Chemical | ChemComp-MG / #87: Chemical | ChemComp-ZN / |
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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: 2.99 Å3/Da / Density % sol: 58.84 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Tris-Acetate pH 7.0, 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: 3.4→49.993 Å / Num. obs: 1009263 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 89.08 Å2 / Rmerge F obs: 0.975 / Rmerge(I) obs: 0.348 / Rrim(I) all: 0.382 / Χ2: 0.865 / Net I/σ(I): 5.32 / Num. measured all: 4845359 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4V88 Resolution: 3.4→49.993 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.27 / 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: 550 Å2 / Biso mean: 78.4438 Å2 / Biso min: 17.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→49.993 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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