+Open data
-Basic information
Entry | Database: PDB / ID: 1kgy | ||||||
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Title | Crystal Structure of the EphB2-ephrinB2 complex | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE RECEPTOR / Developmental protein / TRANSFERASE-TRANSFERASE RECEPTOR COMPLEX | ||||||
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 / venous blood vessel morphogenesis / EPHB-mediated forward signaling ...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 / venous blood vessel morphogenesis / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity / nephric duct morphogenesis / regulation of body fluid levels / urogenital system development / postsynaptic membrane assembly / optic nerve morphogenesis / tight junction assembly / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / neuron projection retraction / axon guidance receptor activity / central nervous system projection neuron axonogenesis / transmembrane-ephrin receptor activity / negative regulation of axonogenesis / positive regulation of long-term neuronal synaptic plasticity / presynapse assembly / dendritic spine development / lymph vessel development / corpus callosum development / positive regulation of synaptic plasticity / camera-type eye morphogenesis / positive regulation of dendritic spine morphogenesis / ephrin receptor activity / regulation of filopodium assembly / regulation of chemotaxis / regulation of behavioral fear response / regulation of autophagosome assembly / commissural neuron axon guidance / positive regulation of protein localization to cell surface / negative regulation of cell adhesion / dendritic spine morphogenesis / negative regulation of Ras protein signal transduction / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / axonal fasciculation / positive regulation of synapse assembly / adherens junction organization / regulation of receptor signaling pathway via JAK-STAT / blood vessel morphogenesis / positive regulation of immunoglobulin production / inner ear morphogenesis / regulation of synapse assembly / regulation of axonogenesis / retinal ganglion cell axon guidance / B cell activation / roof of mouth development / regulation of blood coagulation / regulation of neuronal synaptic plasticity / regulation of postsynaptic membrane neurotransmitter receptor levels / keratinocyte proliferation / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / negative regulation of keratinocyte proliferation / positive regulation of B cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / ephrin receptor binding / phosphorylation / positive regulation of protein localization to plasma membrane / hippocampal mossy fiber to CA3 synapse / axonogenesis / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / axon guidance / receptor protein-tyrosine kinase / adherens junction / animal organ morphogenesis / postsynaptic density membrane / negative regulation of protein kinase activity / cell morphogenesis / peptidyl-tyrosine phosphorylation / Schaffer collateral - CA1 synapse / negative regulation of ERK1 and ERK2 cascade / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / negative regulation of neuron projection development / signaling receptor activity / presynaptic membrane / amyloid-beta binding / protein tyrosine kinase activity / cellular response to lipopolysaccharide / postsynaptic membrane / angiogenesis / postsynapse / learning or memory / dendritic spine / cell adhesion / positive regulation of cell migration / axon Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Himanen, J.P. / Rajashankar, K.R. / Lackmann, M. / Cowan, C.A. / Henkemeyer, M. / Nikolov, D.B. | ||||||
Citation | Journal: Nature / Year: 2001 Title: Crystal structure of an Eph receptor-ephrin complex. Authors: Himanen, J.P. / Rajashankar, K.R. / Lackmann, M. / Cowan, C.A. / 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 | 1kgy.cif.gz | 256.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kgy.ent.gz | 213 KB | Display | PDB format |
PDBx/mmJSON format | 1kgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kgy_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 1kgy_full_validation.pdf.gz | 492.4 KB | Display | |
Data in XML | 1kgy_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 1kgy_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/1kgy ftp://data.pdbj.org/pub/pdb/validation_reports/kg/1kgy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | chains B and F form a heterodimer chains C and D form a heterodimer Chains B, C, F, and G form a proposed heterotetramer |
-Components
#1: Protein | Mass: 20856.512 Da / Num. of mol.: 4 / Fragment: ligand-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P54763, EC: 2.7.1.112 #2: Protein | Mass: 15715.984 Da / Num. of mol.: 4 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P52800 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.98 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6 M Na/K Phosphate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2000 |
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. all: 43549 / Num. obs: 42156 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 2.7→2.82 Å / Rmerge(I) obs: 0.37 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→25 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→25 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.243 / Rfactor Rfree: 0.295 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |