+Open data
-Basic information
Entry | Database: PDB / ID: 3gxu | ||||||
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Title | Crystal structure of Eph receptor and ephrin complex | ||||||
Components |
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Keywords | 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 | Function and homology information DH domain binding / neuron projection fasciculation / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / positive regulation of Rho guanyl-nucleotide exchange factor activity / neuron projection guidance / venous blood vessel morphogenesis / nephric duct morphogenesis / regulation of synapse pruning ...DH domain binding / neuron projection fasciculation / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / positive regulation of Rho guanyl-nucleotide exchange factor activity / neuron projection guidance / venous blood vessel morphogenesis / nephric duct morphogenesis / regulation of synapse pruning / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / PH domain binding / glial cell migration / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / lymph vessel development / negative regulation of epithelial to mesenchymal transition / regulation of chemotaxis / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / regulation of postsynaptic neurotransmitter receptor internalization / adult walking behavior / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Ephrin signaling / blood vessel morphogenesis / Somitogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / regulation of postsynaptic membrane neurotransmitter receptor levels / negative regulation of long-term synaptic potentiation / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / positive regulation of cell adhesion / anatomical structure morphogenesis / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / positive regulation of protein tyrosine kinase activity / axon terminus / axonal growth cone / EPHB-mediated forward signaling / protein tyrosine kinase binding / T cell costimulation / ephrin receptor binding / negative regulation of cell migration / dendritic shaft / filopodium / axon guidance / postsynaptic density membrane / adherens junction / animal organ morphogenesis / neuromuscular junction / Schaffer collateral - CA1 synapse / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / negative regulation of neuron projection development / virus receptor activity / cell-cell signaling / presynaptic membrane / amyloid-beta binding / kinase activity / perikaryon / early endosome membrane / protein tyrosine kinase activity / mitochondrial outer membrane / negative regulation of translation / dendritic spine / protein autophosphorylation / protein stabilization / cell adhesion / protein kinase activity / positive regulation of cell migration / axon / focal adhesion / dendrite / glutamatergic synapse / positive regulation of cell population proliferation / cell surface / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Qin, H.N. / Song, J.X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 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: Journal: J.Biol.Chem. / Year: 2008 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: 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 | 3gxu.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gxu.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gxu ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gxu | HTTPS FTP |
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-Related 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: 20206.844 Da / Num. of mol.: 1 / Fragment: UNP residues 29-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA4, HEK8, SEK, TYRO1 / Plasmid: PET32a / Production host: Escherichia coli (E. coli) 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.) Homo sapiens (human) / Gene: EFNB2, EPLG5, HTKL, LERK5 / Plasmid: PET32a / Production host: Escherichia coli (E. coli) / References: UniProt: P52799 |
#3: 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: 2.21 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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