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- PDB-7osm: Intermediate translocation complex of 80 S.cerevisiae ribosome wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7osm | ||||||
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Title | Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands | ||||||
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![]() | RIBOSOME / translocation / eEF2 / tRNA / mRNA / eukaryotic ribosome | ||||||
Function / homology | ![]() ribosomal subunit / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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) / L13a-mediated translational silencing of Ceruloplasmin expression ...ribosomal subunit / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / translation elongation factor activity / 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) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / modification-dependent protein catabolic process / rRNA processing / large ribosomal subunit / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / RNA binding / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Djumagulov, M. / Jenner, L. / Rozov, A. / Demeshkina, N. / Yusupov, M. / Yusupova, G. | ||||||
![]() | ![]() Title: Accuracy mechanism of eukaryotic ribosome translocation. Authors: Djumagulov, M. / Demeshkina, N. / Jenner, L. / Rozov, A. / Yusupov, M. / Yusupova, G. #1: ![]() Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Adams, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 5.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 517.2 KB | Display | |
Data in CIF | ![]() | 758 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7osaC ![]() 4v88S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-RNA chain , 7 types, 7 molecules 25SAB58S18SASITPSITmRNA
#1: RNA chain | Mass: 1097492.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#46: RNA chain | Mass: 579126.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#80: RNA chain | Mass: 24726.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#81: RNA chain | Mass: 24801.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#82: RNA chain | Mass: 2511.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
+Protein , 25 types, 25 molecules uL10uL4uL5uL22eL18eL21eL30eL31eL32eL33uL29eL37eL38eL40eL42uS3uS7uS4uS9eS17eS28uS14RACKeS31eEF2
+60S ribosomal protein ... , 27 types, 27 molecules uL2uL3uL18eL6uL30eL8uL6uL16eL13eL14eL15uL13eL19eL20eL22uL14eL24uL23uL24eL27uL15eL29eL34eL36eL39eL43uL11
-Protein/peptide , 1 types, 1 molecules eL41
#43: Protein/peptide | Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+40S ribosomal protein ... , 23 types, 23 molecules uS2eS1uS5eS4eS6eS7eS8eS10uS17uS15uS11uS19uS13eS19uS10eS21uS8uS12eS24eS25eS26eS27eS30
-Non-polymers , 3 types, 508 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
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![](data/chem/img/GTP.gif)
#84: Chemical | ChemComp-MG / #85: Chemical | ChemComp-ZN / #86: Chemical | ChemComp-GTP / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, KSCN, Tris-HAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→149.93 Å / Num. obs: 712272 / % possible obs: 99.99 % / Redundancy: 172 % / Biso Wilson estimate: 105.49 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.35 |
Reflection shell | Resolution: 3.2→3.314 Å / Mean I/σ(I) obs: 0.94 / Num. unique obs: 58317 / CC1/2: 0.14 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4V88 Resolution: 3→149.93 Å / SU ML: 0.8588 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.5857 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→149.93 Å
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Refine LS restraints |
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LS refinement shell |
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