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Open data
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Basic information
Entry | Database: PDB / ID: 2wo2 | ||||||
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Title | Crystal Structure of the EphA4-ephrinB2 complex | ||||||
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![]() | TRANSFERASE/SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN COMPLEX / OSTEOGENESIS / AXON GUIDANCE / CELL SURFACE RECEPTOR / DEVELOPMENTAL PROTEIN / NEUROGENESIS / CELL SIGNALING | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Bowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structural Plasticity of Eph-Receptor A4 Facilitates Cross-Class Ephrin Signalling Authors: Bowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.5 KB | Display | ![]() |
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PDB format | ![]() | 58.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.4 KB | Display | ![]() |
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Full document | ![]() | 465.4 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wo1C ![]() 2wo3C ![]() 1kgyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21467.191 Da / Num. of mol.: 1 / Fragment: EPHRIN LIGAND BINDING DOMAIN, RESIDUES 30-202 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: 17506.854 Da / Num. of mol.: 1 / Fragment: EPH RECEPTOR BINDING DOMAIN, RESIDUES 27-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39.6 % / Description: NONE |
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Crystal grow | pH: 6 Details: 30% PEG 6000, 1 M LITHIUM CHLORIDE, AND 100 MM MES PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 11645 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 60.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 43.2 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.6 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KGY Resolution: 2.45→28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 26.32 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.054 / ESU R Free: 0.315 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.394 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→28 Å
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