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Open data
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Basic information
Entry | Database: PDB / ID: 3gxu | ||||||
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Title | Crystal structure of Eph receptor and ephrin complex | ||||||
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![]() | TRANSFERASE / Complex structure / Eph / ephrin / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase / Developmental protein / Differentiation / Disulfide bond / Host-virus interaction / Neurogenesis | ||||||
Function / homology | ![]() DH domain binding / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / neuron projection guidance / venous blood vessel morphogenesis / nephric duct morphogenesis / fasciculation of sensory neuron axon ...DH domain binding / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / neuron projection guidance / venous blood vessel morphogenesis / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / regulation of synapse pruning / positive regulation of aorta morphogenesis / synapse pruning / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of cardiac muscle cell differentiation / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / glial cell migration / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / lymph vessel development / regulation of chemotaxis / regulation of dendritic spine morphogenesis / transmembrane-ephrin receptor activity / negative regulation of cell adhesion / negative regulation of epithelial to mesenchymal transition / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / adult walking behavior / motor neuron axon guidance / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / blood vessel morphogenesis / Ephrin signaling / Somitogenesis / positive regulation of amyloid-beta formation / regulation of axonogenesis / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / regulation of postsynaptic membrane neurotransmitter receptor levels / keratinocyte proliferation / positive regulation of protein tyrosine kinase activity / positive regulation of cell adhesion / negative regulation of long-term synaptic potentiation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / negative regulation of keratinocyte proliferation / anatomical structure morphogenesis / axonal growth cone / axon terminus / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / negative regulation of cell migration / protein tyrosine kinase binding / dendritic shaft / filopodium / adherens junction / animal organ morphogenesis / postsynaptic density membrane / axon guidance / Schaffer collateral - CA1 synapse / neuromuscular junction / receptor protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / cell-cell signaling / negative regulation of neuron projection development / presynaptic membrane / kinase activity / virus receptor activity / amyloid-beta binding / early endosome membrane / perikaryon / protein tyrosine kinase activity / mitochondrial outer membrane / protein autophosphorylation / dendritic spine / protein stabilization / negative regulation of translation / cell adhesion / protein kinase activity / positive regulation of cell migration / axon / focal adhesion / glutamatergic synapse / dendrite / positive regulation of cell population proliferation / cell surface / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Qin, H.N. / Song, J.X. | ||||||
![]() | ![]() Title: Structural characterization of the EphA4-ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity Authors: Qin, H. / Noberini, R. / Huan, X. / Shi, J. / Pasquale, E.B. / Song, J. #1: ![]() Title: Crystal structure and NMR binding reveal that two small molecule antagonists target the high affinity ephrin-binding channel of the EphA4 receptor Authors: Qin, H. / Shi, J. / Noberini, R. / Pasquale, E.B. / Song, J. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.6 KB | Display | ![]() |
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PDB format | ![]() | 61.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.9 KB | Display | ![]() |
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Full document | ![]() | 429.2 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 20206.844 Da / Num. of mol.: 1 / Fragment: UNP residues 29-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P54764, receptor protein-tyrosine kinase |
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#2: Protein | Mass: 16261.525 Da / Num. of mol.: 1 / Fragment: UNP residues 27-169 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 23.5% PEG4000, 0.1M Tris, 0.2M MgCl2, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 11071 / Num. obs: 10938 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CKH, 1KGY Resolution: 2.5→25 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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