+Open data
-Basic information
Entry | Database: PDB / ID: 3a62 | ||||||
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Title | Crystal structure of phosphorylated p70S6K1 | ||||||
Components | Ribosomal protein S6 kinase beta-1Ribosome | ||||||
Keywords | TRANSFERASE / Kinase / Kinase domain / Inactive / Active / Ribosomal S6 kinase / Activation / Alternative initiation / ATP-binding / Cell junction / Cytoplasm / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Synapse / Synaptosome | ||||||
Function / homology | Function and homology information long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / phosphatidylinositol-mediated signaling / response to glucagon ...long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / phosphatidylinositol-mediated signaling / response to glucagon / response to testosterone / positive regulation of smooth muscle cell migration / TOR signaling / mTORC1-mediated signalling / germ cell development / positive regulation of translational initiation / skeletal muscle contraction / long-term memory / behavioral fear response / response to tumor necrosis factor / response to glucose / response to mechanical stimulus / negative regulation of insulin receptor signaling pathway / positive regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / response to nutrient levels / protein phosphatase 2A binding / positive regulation of translation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / PDZ domain binding / negative regulation of extrinsic apoptotic signaling pathway / peptide binding / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / modulation of chemical synaptic transmission / response to toxic substance / cellular response to growth factor stimulus / cellular response to type II interferon / cellular response to insulin stimulus / cell migration / postsynapse / peptidyl-serine phosphorylation / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / signal transduction / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Sunami, T. / Byrne, N. / Diehl, R.E. / Funabashi, K. / Hall, D.L. / Ikuta, M. / Patel, S.B. / Shipman, J.M. / Smith, R.F. / Takahashi, I. ...Sunami, T. / Byrne, N. / Diehl, R.E. / Funabashi, K. / Hall, D.L. / Ikuta, M. / Patel, S.B. / Shipman, J.M. / Smith, R.F. / Takahashi, I. / Zugay-Murphy, J. / Iwasawa, Y. / Lumb, K.J. / Munshi, S.K. / Sharma, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural basis of human p70 ribosomal S6 kinase-1 regulation by activation loop phosphorylation. Authors: Sunami, T. / Byrne, N. / Diehl, R.E. / Funabashi, K. / Hall, D.L. / Ikuta, M. / Patel, S.B. / Shipman, J.M. / Smith, R.F. / Takahashi, I. / Zugay-Murphy, J. / Iwasawa, Y. / Lumb, K.J. / Munshi, S.K. / Sharma, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a62.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a62.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 3a62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/3a62 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/3a62 | HTTPS FTP |
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-Related structure data
Related structure data | 3a60SC 3a61C 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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Unit cell |
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-Components
#1: Protein | Mass: 37016.621 Da / Num. of mol.: 1 / Fragment: UNP residues 75-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVL1392 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P23443, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-STU / |
#3: Chemical | ChemComp-MN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.69 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris, pH 8.5, 3.5M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→29.01 Å / Num. obs: 15108 / % possible obs: 99.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 38.1 Å2 / Rsym value: 0.05 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 8.19 / Rsym value: 0.308 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A60 Resolution: 2.35→29.01 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1654444.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.242 Å2 / ksol: 0.367269 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→29.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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