+Open data
-Basic information
Entry | Database: PDB / ID: 2pa2 | ||||||
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Title | Crystal structure of human Ribosomal protein L10 core domain | ||||||
Components | 60S ribosomal protein L10 | ||||||
Keywords | RIBOSOMAL PROTEIN / ribosomal protein L10 / QM protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information embryonic brain development / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...embryonic brain development / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / regulation of translation / cytoplasmic translation / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein-containing complex / RNA binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nishimura, M. / Kaminishi, T. / Takemoto, C. / Kawazoe, M. / Yoshida, T. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Ohkubo, T. / Yokoyama, S. ...Nishimura, M. / Kaminishi, T. / Takemoto, C. / Kawazoe, M. / Yoshida, T. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Ohkubo, T. / Yokoyama, S. / Kobayashi, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal Structure of Human Ribosomal Protein L10 Core Domain Reveals Eukaryote-Specific Motifs in Addition to the Conserved Fold Authors: Nishimura, M. / Kaminishi, T. / Takemoto, C. / Kawazoe, M. / Yoshida, T. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Ohkubo, T. / Yokoyama, S. / Kobayashi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pa2.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pa2.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/2pa2 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/2pa2 | HTTPS FTP |
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-Related structure data
Related structure data | 1s72S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17195.111 Da / Num. of mol.: 2 / Fragment: core domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32b-L10CD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27635 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 43.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 1.0M di-sodium hydroxyl phosphate, 1.0M potassium dihydroxyl phosphate, pH 4.5 100mM sodium acetate , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2006 / Details: rhodium-coated mirrors |
Radiation | Monochromator: Rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 10870 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 60 Å2 / Rsym value: 0.05 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.62 / Num. unique all: 1019 / Rsym value: 0.438 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S72 chain H Resolution: 2.5→45.66 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 890089.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1449 Å2 / ksol: 0.380904 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→45.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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