[English] 日本語
Yorodumi- PDB-3fy2: Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fy2 | ||||||
---|---|---|---|---|---|---|---|
Title | Human EphA3 Kinase and Juxtamembrane Region Bound to Substrate KQWDNYEFIW | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / receptor tyrosine kinase / juxtamembrane segment / structural genomics / peptide co-crystal structure / Structural Genomics Consortium / SGC / ATP-binding / Cell membrane / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information fasciculation of sensory neuron axon / fasciculation of motor neuron axon / transmembrane-ephrin receptor activity / regulation of epithelial to mesenchymal transition / GPI-linked ephrin receptor activity / ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity ...fasciculation of sensory neuron axon / fasciculation of motor neuron axon / transmembrane-ephrin receptor activity / regulation of epithelial to mesenchymal transition / GPI-linked ephrin receptor activity / ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to retinoic acid / axon guidance / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / actin cytoskeleton / cell migration / nuclear membrane / early endosome / cell adhesion / dendrite / extracellular region / nucleoplasm / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Davis, T. / Walker, J.R. / Mackenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Febs J. / Year: 2009 Title: Structural recognition of an optimized substrate for the ephrin family of receptor tyrosine kinases. Authors: Davis, T.L. / Walker, J.R. / Allali-Hassani, A. / Parker, S.A. / Turk, B.E. / Dhe-Paganon, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fy2.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fy2.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fy2 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fy2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3fxxSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | BIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT |
-Components
#1: Protein | Mass: 41819.730 Da / Num. of mol.: 1 Fragment: Juxtamembrane segment and kinase domain: residues 577-947 Mutation: Y608A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA3, ETK, ETK1, HEK, TYRO4 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P29320, receptor protein-tyrosine kinase |
---|---|
#2: Protein/peptide | Mass: 1429.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 30.9 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 mg/mL Protein, 25% PEG 3350, 0.04M Ammonium sulfate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 2, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→34.04 Å / Num. all: 29459 / Num. obs: 29456 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.842 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 7.855 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 35.85 / Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FXX Resolution: 1.8→26.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.87 / SU B: 2.345 / SU ML: 0.076 / SU R Cruickshank DPI: 0.13 / SU Rfree: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 60.56 Å2 / Biso mean: 29.522 Å2 / Biso min: 11.92 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.121 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→26.73 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|