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Open data
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Basic information
Entry | Database: PDB / ID: 4v88 | ||||||||||||
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Title | The structure of the eukaryotic ribosome at 3.0 A resolution. | ||||||||||||
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![]() | RIBOSOME / Translation / 40S / 60S / 80S / ribosomal / ribosomal RNA / rRNA / ribosomal protein / STM1 / eukaryotic ribosome / RNA-protein complex | ||||||||||||
Function / homology | ![]() 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 / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / translational elongation / 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 / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / TOR signaling / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / ribosomal small subunit export from nucleus / translation regulator activity / ribosomal subunit export from nucleus / translational termination / 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / telomere maintenance / ribosome assembly / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / 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 / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / ribosomal large subunit assembly / cytoplasmic stress granule / modification-dependent protein catabolic process / 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 / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / RNA binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ben-Shem, A. / Garreau de Loubresse, N. / Melnikov, S. / Jenner, L. / Yusupova, G. / Yusupov, M. | ||||||||||||
![]() | ![]() Title: The structure of the eukaryotic ribosome at 3.0 angstrom resolution. Authors: Ben-Shem, A. / Garreau de Loubresse, N. / Melnikov, S. / Jenner, L. / Yusupova, G. / Yusupov, M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 11.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.6 MB | Display | ![]() |
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Full document | ![]() | 11.2 MB | Display | |
Data in XML | ![]() | 1.1 MB | Display | |
Data in CIF | ![]() | 1.6 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3o2z ![]() 3o30 ![]() 3o58 ![]() 3o5h 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-RNA chain , 5 types, 8 molecules A2A1A5A3A7A4A8A6
#1: RNA chain | Mass: 577937.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
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#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) ![]() ![]() #80: RNA chain | | Mass: 576517.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+40S ribosomal protein ... , 32 types, 64 molecules AACAABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCO...
-Protein , 2 types, 3 molecules AgCgDq
#34: Protein | Mass: 34841.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #83: Protein | | Mass: 33289.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Suppressor protein ... , 2 types, 2 molecules AhCh
#35: Protein | Mass: 29052.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#81: Protein | Mass: 29153.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+60S ribosomal protein ... , 41 types, 82 molecules BADABBDBBCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBLDLBMDMBNDNBODOBPDP...
-Ribosomal protein ... , 3 types, 3 molecules DKDrDs
#82: Protein | Mass: 13209.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#84: Protein/peptide | Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#85: Protein/peptide | Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 4 types, 3568 molecules ![](data/chem/img/OHX.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#86: Chemical | ChemComp-OHX / #87: Chemical | ChemComp-MG / #88: Chemical | ChemComp-ZN / #89: Water | ChemComp-HOH / | |
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-Details
Sequence details | SEQUENCE DATABASE REFERENCE: UNS542419065 FOR CHAIN 2. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→300 Å / Num. all: 1639983 / Num. obs: 1639309 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 38.4 % / Biso Wilson estimate: 63 Å2 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 3→3.1 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3O2Z, 3O30, 3O58, 3O5H Resolution: 3→300 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: RESIDUE 1756 (1493 ACCORDING TO E.COLI NUMBERING) WAS MODELLED IN TWO ALTERNATIVE CONFORMATIONS.
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Displacement parameters | Biso mean: 63 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→300 Å
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Refine LS restraints |
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