+Open data
-Basic information
Entry | Database: PDB / ID: 1k3a | ||||||
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Title | Structure of the Insulin-like Growth Factor 1 Receptor Kinase | ||||||
Components |
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Keywords | TRANSFERASE / protein kinase / tyrosine kinase / tyrosine phosphorylation / protein-substrate complex | ||||||
Function / homology | Function and homology information cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / protein kinase complex / positive regulation of steroid hormone biosynthetic process / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / protein kinase complex / positive regulation of steroid hormone biosynthetic process / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / insulin receptor complex / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / insulin-like growth factor I binding / positive regulation of glucose metabolic process / insulin receptor activity / transcytosis / Activated NTRK3 signals through PI3K / response to alkaloid / alphav-beta3 integrin-IGF-1-IGF1R complex / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of protein-containing complex disassembly / cellular response to angiotensin / Signaling by Leptin / PI3K/AKT activation / cellular response to insulin-like growth factor stimulus / response to L-glutamate / dendritic spine maintenance / cellular response to fatty acid / insulin binding / Signaling by ALK / establishment of cell polarity / IRS activation / negative regulation of MAPK cascade / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / regulation of JNK cascade / estrous cycle / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / insulin receptor substrate binding / PI3K Cascade / G-protein alpha-subunit binding / negative regulation of insulin secretion / response to vitamin E / positive regulation of glycogen biosynthetic process / SHC-related events triggered by IGF1R / Signal attenuation / phosphatidylinositol 3-kinase binding / positive regulation of insulin receptor signaling pathway / Growth hormone receptor signaling / peptidyl-tyrosine autophosphorylation / negative regulation of insulin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / T-tubule / insulin-like growth factor receptor binding / cerebellum development / Interleukin-7 signaling / phosphotyrosine residue binding / cellular response to dexamethasone stimulus / axonogenesis / insulin-like growth factor receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to nicotine / SH2 domain binding / cellular response to estradiol stimulus / caveola / protein kinase C binding / hippocampus development / positive regulation of glucose import / positive regulation of smooth muscle cell proliferation / cellular response to glucose stimulus / response to insulin / insulin receptor binding / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / cellular response to insulin stimulus / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / signaling receptor complex adaptor activity / cellular senescence / glucose homeostasis / PIP3 activates AKT signaling / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / response to ethanol / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Favelyukis, S. / Till, J.H. / Hubbard, S.R. / Miller, W.T. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Structure and autoregulation of the insulin-like growth factor 1 receptor kinase. Authors: Favelyukis, S. / Till, J.H. / Hubbard, S.R. / Miller, W.T. | ||||||
History |
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Remark 999 | SEQUENCE THE RESIDUE CORRESPONDS TO RESIDUE FROM A SYNTHETIC PEPTIDE. IT WAS ADDED TO MODIFY THE ...SEQUENCE THE RESIDUE CORRESPONDS TO RESIDUE FROM A SYNTHETIC PEPTIDE. IT WAS ADDED TO MODIFY THE SEQUENCE TO BE SUITABLE FOR ACTIVITY ASSAYS |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k3a.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k3a.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/1k3a ftp://data.pdbj.org/pub/pdb/validation_reports/k3/1k3a | HTTPS FTP |
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-Related structure data
Related structure data | 1ir3S 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 | tetramer of 2 alpha and 2 beta chains linked by disulfide bonds. |
-Components
#1: Protein | Mass: 34410.199 Da / Num. of mol.: 1 / Fragment: beta chain, kinase domain (residues 988-1286) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFast-Bac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P08069, EC: 2.7.1.112 |
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#2: Protein/peptide | Mass: 1598.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P35568 |
#3: Chemical | ChemComp-ACP / |
#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: 2.9 Å3/Da / Density % sol: 57.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9725 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2001 |
Radiation | Monochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9725 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.07 Å / Num. all: 24941 / Num. obs: 24941 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.048 |
Reflection shell | Resolution: 2.1→2.18 Å / Rsym value: 0.254 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 279673 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.254 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ir3 Resolution: 2.1→28.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 387254.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.8196 Å2 / ksol: 0.357892 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.248 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.275 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.231 |