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Yorodumi- PDB-4l3l: Crystal structures of human p70S6K1 kinase domain (Zinc anomalous) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l3l | ||||||
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Title | Crystal structures of human p70S6K1 kinase domain (Zinc anomalous) | ||||||
Components | RPS6KB1 protein | ||||||
Keywords | TRANSFERASE / Protein kinase | ||||||
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 / response to glucagon / response to testosterone ...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 / response to glucagon / response to testosterone / positive regulation of smooth muscle cell migration / germ cell development / mTORC1-mediated signalling / phosphatidylinositol-mediated signaling / skeletal muscle contraction / TOR signaling / behavioral fear response / positive regulation of translational initiation / response to tumor necrosis factor / cellular response to dexamethasone stimulus / long-term memory / 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 / positive regulation of mitotic cell cycle / response to nutrient levels / positive regulation of smooth muscle cell proliferation / peptide binding / protein phosphatase 2A binding / positive regulation of translation / PDZ domain binding / negative regulation of extrinsic apoptotic signaling pathway / modulation of chemical synaptic transmission / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / response to toxic substance / cellular response to type II interferon / cellular response to growth factor stimulus / cell migration / peptidyl-serine phosphorylation / response to ethanol / mitochondrial outer membrane / postsynapse / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / cell surface / signal transduction / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wang, J. / Zhong, C. / Ding, J. | ||||||
Citation | Journal: Biochem.J. / Year: 2013 Title: Crystal structures of S6K1 provide insights into the regulation mechanism of S6K1 by the hydrophobic motif Authors: Wang, J. / Zhong, C. / Wang, F. / Qu, F. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l3l.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l3l.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 4l3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l3l_validation.pdf.gz | 732.9 KB | Display | wwPDB validaton report |
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Full document | 4l3l_full_validation.pdf.gz | 736.4 KB | Display | |
Data in XML | 4l3l_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 4l3l_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/4l3l ftp://data.pdbj.org/pub/pdb/validation_reports/l3/4l3l | HTTPS FTP |
-Related structure data
Related structure data | 4l3jC 4l42C 4l43C 4l44C 4l45C 4l46C 3a62S C: citing same article (ref.) S: Starting model for refinement |
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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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Details | biological unit is monomer |
-Components
#1: Protein | Mass: 34337.094 Da / Num. of mol.: 1 / Fragment: UNP residues 88-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1, hCG_1815774 / Plasmid: pFastBacHTB / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Spodoptera frugiperda / References: UniProt: Q7Z721, UniProt: P23443*PLUS |
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#2: Chemical | ChemComp-5FI / |
#3: Chemical | ChemComp-ZN / |
#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: 2.61 Å3/Da / Density % sol: 52.88 % / Mosaicity: 0.452 ° |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.5M sodium formate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2826 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: CCD ADSC unsupported-q315 / Detector: CCD / Date: May 20, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2826 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 8.9 % / Av σ(I) over netI: 22.51 / Number: 181839 / Rmerge(I) obs: 0.121 / Χ2: 1.82 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 20480 / % possible obs: 96.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 20480 / % possible obs: 96.3 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.121 / Χ2: 1.817 / Net I/σ(I): 12.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A62 Resolution: 2.1→46.48 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.031 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.45 Å2 / Biso mean: 56.1127 Å2 / Biso min: 27.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -12.0547 Å / Origin y: 20.0145 Å / Origin z: 4.8641 Å
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