[English] 日本語
Yorodumi- PDB-4r7h: Crystal structure of FMS KINASE domain with a small molecular inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r7h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of FMS KINASE domain with a small molecular inhibitor, PLX3397 | ||||||
Components | Macrophage colony-stimulating factor 1 receptor | ||||||
Keywords | transferase/transferase inhibitor / CSF-1-R / FMS proto-oncogene / C-FMS / CD115 antigen / kinase / ATP-binding / PLX3397 / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / microglial cell proliferation / olfactory bulb development / mammary gland duct morphogenesis ...macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / microglial cell proliferation / olfactory bulb development / mammary gland duct morphogenesis / positive regulation by host of viral process / ruffle organization / positive regulation of macrophage proliferation / regulation of bone resorption / positive regulation of cell motility / Other interleukin signaling / positive regulation of macrophage chemotaxis / growth factor binding / cellular response to cytokine stimulus / cytokine binding / monocyte differentiation / regulation of MAPK cascade / macrophage differentiation / hemopoiesis / positive regulation of protein tyrosine kinase activity / Transcriptional Regulation by VENTX / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / axon guidance / response to ischemia / regulation of actin cytoskeleton organization / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / protein phosphatase binding / protein tyrosine kinase activity / cell population proliferation / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / signal transduction / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8001 Å | ||||||
Authors | Zhang, Y. / Zhang, K. / Zhang, C. | ||||||
Citation | Journal: N Engl J Med / Year: 2015 Title: Structure-Guided Blockade of CSF1R Kinase in Tenosynovial Giant-Cell Tumor. Authors: Tap, W.D. / Wainberg, Z.A. / Anthony, S.P. / Ibrahim, P.N. / Zhang, C. / Healey, J.H. / Chmielowski, B. / Staddon, A.P. / Cohn, A.L. / Shapiro, G.I. / Keedy, V.L. / Singh, A.S. / Puzanov, I. ...Authors: Tap, W.D. / Wainberg, Z.A. / Anthony, S.P. / Ibrahim, P.N. / Zhang, C. / Healey, J.H. / Chmielowski, B. / Staddon, A.P. / Cohn, A.L. / Shapiro, G.I. / Keedy, V.L. / Singh, A.S. / Puzanov, I. / Kwak, E.L. / Wagner, A.J. / Von Hoff, D.D. / Weiss, G.J. / Ramanathan, R.K. / Zhang, J. / Habets, G. / Zhang, Y. / Burton, E.A. / Visor, G. / Sanftner, L. / Severson, P. / Nguyen, H. / Kim, M.J. / Marimuthu, A. / Tsang, G. / Shellooe, R. / Gee, C. / West, B.L. / Hirth, P. / Nolop, K. / van de Rijn, M. / Hsu, H.H. / Peterfy, C. / Lin, P.S. / Tong-Starksen, S. / Bollag, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4r7h.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4r7h.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 4r7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/4r7h ftp://data.pdbj.org/pub/pdb/validation_reports/r7/4r7h | HTTPS FTP |
---|
-Related structure data
Related structure data | 4r7iC 4hw7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38640.176 Da / Num. of mol.: 1 / Fragment: FMS kinase domain with KID (UNP residues 538-919) / Mutation: C667T, C830S, C907T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSF1R, FMS / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P07333, receptor protein-tyrosine kinase |
---|---|
#2: Chemical | ChemComp-P31 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.81 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG8K, 0.2M MGCL AND 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2008 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60.471 Å / Num. all: 10121 / Num. obs: 10071 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HW7 Resolution: 2.8001→52.625 Å / SU ML: 0.35 / σ(F): 1.74 / Phase error: 21.72 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.59 Å2 / ksol: 0.379 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8001→52.625 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|