+Open data
-Basic information
Entry | Database: PDB / ID: 2wo2 | ||||||
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Title | Crystal Structure of the EphA4-ephrinB2 complex | ||||||
Components |
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Keywords | TRANSFERASE/SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN COMPLEX / OSTEOGENESIS / AXON GUIDANCE / CELL SURFACE RECEPTOR / DEVELOPMENTAL PROTEIN / NEUROGENESIS / CELL SIGNALING | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Bowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y. | ||||||
Citation | Journal: Structure / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wo2.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wo2.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wo2 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wo2 | HTTPS FTP |
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-Related structure data
Related structure data | 2wo1C 2wo3C 1kgyS C: citing same article (ref.) S: Starting model for refinement |
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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: 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.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) 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.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P52799 |
#3: Sugar | ChemComp-NAG / |
#4: 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 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.977 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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