+Open data
-Basic information
Entry | Database: PDB / ID: 1shw | |||||||||
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Title | EphB2 / EphrinA5 Complex Structure | |||||||||
Components |
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Keywords | hormone/growth factor/receptor / receptor tyrosine kinase / ephrin signaling / hormone-growth factor-receptor COMPLEX | |||||||||
Function / homology | Function and homology information neurotrophin TRKB receptor binding / 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 / EPHA-mediated growth cone collapse / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells ...neurotrophin TRKB receptor binding / 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 / EPHA-mediated growth cone collapse / 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 / negative regulation of substrate adhesion-dependent cell spreading / axon guidance receptor activity / central nervous system projection neuron axonogenesis / synaptic membrane adhesion / regulation of cell-cell adhesion / negative regulation of axonogenesis / regulation of behavioral fear response / transmembrane-ephrin receptor activity / positive regulation of long-term neuronal synaptic plasticity / collateral sprouting / regulation of autophagosome assembly / positive regulation of dendritic spine morphogenesis / cellular response to follicle-stimulating hormone stimulus / dendritic spine development / corpus callosum development / positive regulation of collateral sprouting / positive regulation of synaptic plasticity / camera-type eye morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of filopodium assembly / ephrin receptor activity / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / chemorepellent activity / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / regulation of cell morphogenesis / 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 focal adhesion assembly / regulation of neuronal synaptic plasticity / regulation of axonogenesis / B cell activation / regulation of GTPase activity / roof of mouth development / regulation of blood coagulation / positive regulation of immunoglobulin production / basement membrane / GABA-ergic synapse / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / regulation of microtubule cytoskeleton organization / positive regulation of B cell proliferation / cellular response to forskolin / hippocampal mossy fiber to CA3 synapse / ephrin receptor binding / axonogenesis / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / caveola / cell periphery / axon guidance / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / adherens junction / 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 peptidyl-tyrosine phosphorylation / 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 Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Himanen, J.P. / Chumley, M.J. / Lackmann, M. / Li, C. / Barton, W.A. / Jeffrey, P.D. / Vearing, C. / Geleick, D. / Feldheim, D.A. / Boyd, A.W. | |||||||||
Citation | Journal: Nat.Neurosci. / Year: 2004 Title: Repelling class discrimination: ephrin-A5 binds to and activates EphB2 receptor signaling Authors: Himanen, J.P. / Chumley, M.J. / Lackmann, M. / Li, C. / Barton, W.A. / Jeffrey, P.D. / Vearing, C. / Geleick, D. / Feldheim, D.A. / Boyd, A.W. / Henkemeyer, M. / Nikolov, D.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1shw.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1shw.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 1shw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/1shw ftp://data.pdbj.org/pub/pdb/validation_reports/sh/1shw | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 16320.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: EFNA5, EPLG7, LERK7, EPL7 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08543 |
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#2: Protein | Mass: 20884.564 Da / Num. of mol.: 1 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 (DE3) / References: UniProt: P54763 |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose |
#4: Chemical | ChemComp-ZN / |
#5: 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: 2.78 Å3/Da / Density % sol: 55.76 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 1, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 21816 / Num. obs: 21147 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2→2.09 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EphB2/ EphrinB2 Resolution: 2.2→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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