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Yorodumi- PDB-3etp: The crystal structure of the ligand-binding domain of the EphB2 r... -
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-Basic information
Entry | Database: PDB / ID: 3etp | ||||||
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Title | The crystal structure of the ligand-binding domain of the EphB2 receptor at 2.0 A resolution | ||||||
Components | Ephrin type-B receptor 2 | ||||||
Keywords | TRANSFERASE / Eph receptor / tyrosine kinase / Alternative splicing / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / negative regulation of NMDA glutamate receptor activity / EPH-Ephrin signaling / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity ...regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / negative regulation of NMDA glutamate receptor activity / EPH-Ephrin signaling / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity / postsynaptic membrane assembly / urogenital system development / regulation of body fluid levels / optic nerve morphogenesis / tight junction assembly / neuron projection retraction / axon guidance receptor activity / central nervous system projection neuron axonogenesis / negative regulation of axonogenesis / regulation of behavioral fear response / transmembrane-ephrin receptor activity / positive regulation of long-term neuronal synaptic plasticity / regulation of autophagosome assembly / positive regulation of dendritic spine morphogenesis / dendritic spine development / corpus callosum development / positive regulation of synaptic plasticity / camera-type eye morphogenesis / regulation of filopodium assembly / ephrin receptor activity / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / retinal ganglion cell axon guidance / axonal fasciculation / positive regulation of synapse assembly / regulation of receptor signaling pathway via JAK-STAT / regulation of synapse assembly / inner ear morphogenesis / regulation of neuronal synaptic plasticity / regulation of axonogenesis / B cell activation / roof of mouth development / regulation of blood coagulation / positive regulation of immunoglobulin production / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / positive regulation of B cell proliferation / hippocampal mossy fiber to CA3 synapse / axonogenesis / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / axon guidance / positive regulation of protein localization to plasma membrane / animal organ morphogenesis / negative regulation of protein kinase activity / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of tumor necrosis factor production / signaling receptor activity / presynaptic membrane / amyloid-beta binding / postsynaptic membrane / postsynapse / angiogenesis / protein tyrosine kinase activity / cellular response to lipopolysaccharide / dendritic spine / learning or memory / positive regulation of cell migration / axon / phosphorylation / signaling receptor binding / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / positive regulation of gene expression / cell surface / nucleoplasm / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Goldgur, Y. / Paavilainen, S. / Nikolov, D.B. / Himanen, J.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of the ligand-binding domain of the EphB2 receptor at 2 A resolution. Authors: Goldgur, Y. / Paavilainen, S. / Nikolov, D. / Himanen, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3etp.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3etp.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 3etp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/3etp ftp://data.pdbj.org/pub/pdb/validation_reports/et/3etp | HTTPS FTP |
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-Related structure data
Related structure data | 1nukS 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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-Components
#1: Protein | Mass: 21437.211 Da / Num. of mol.: 1 / Fragment: UNP residues 28-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ephb2, Epth3, Nuk, Sek3 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): AD494 References: UniProt: P54763, receptor protein-tyrosine kinase |
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#2: Water | ChemComp-HOH / |
Sequence details | ACCORDING TO THE AUTHORS, THE ELECTRON DENSITY OF THIS WELL ORDERED RESIDUE DOES NOT FIT PHE. IT IS ...ACCORDING TO THE AUTHORS, THE ELECTRON DENSITY OF THIS WELL ORDERED RESIDUE DOES NOT FIT PHE. IT IS PROBABLY A CLONING ARTEFACT. THE ORIGINAL PLASMID WAS SEQUENCED AND HAD EITHER TTC (PHE) OR ATC (ILE) AT THIS POSITION. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 1.2 M Na/K phosphate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.13 Å / Num. obs: 15984 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NUK Resolution: 2→37.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.368 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 42.247 Å2
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Refinement step | Cycle: LAST / Resolution: 2→37.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.054 Å / Total num. of bins used: 20
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