+Open data
-Basic information
Entry | Database: PDB / ID: 2wo3 | |||||||||
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Title | Crystal Structure of the EphA4-ephrinA2 complex | |||||||||
Components |
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Keywords | TRANSFERASE/SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN COMPLEX / EFN / EPH / EPHA4 / KINASE / EPHRIN / COMPLEX / MEMBRANE / CELL SURFACE RECEPTOR / TYROSINE-PROTEIN KINASE / GLYCOPROTEIN / EPHRINA2 | |||||||||
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 / nephric duct morphogenesis / regulation of synapse pruning / fasciculation of sensory neuron axon ...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 / nephric duct morphogenesis / regulation of synapse pruning / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / : / 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 / negative regulation of epithelial to mesenchymal transition / olfactory bulb development / regulation of dendritic spine morphogenesis / bone remodeling / negative regulation of cell adhesion / motor neuron axon guidance / adult walking behavior / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Somitogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / negative regulation of long-term synaptic potentiation / EPH-ephrin mediated repulsion of cells / positive regulation of cell adhesion / ephrin receptor signaling pathway / positive regulation of protein tyrosine kinase activity / axon terminus / axonal growth cone / protein tyrosine kinase binding / ephrin receptor binding / osteoclast differentiation / negative regulation of cell migration / dendritic shaft / filopodium / axon guidance / postsynaptic density membrane / adherens junction / 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 / 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 / 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: 2.35 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED (DSSP). | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED (DSSP). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wo3.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wo3.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 2wo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wo3 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wo3 | HTTPS FTP |
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-Related structure data
Related structure data | 2wo1C 2wo2C 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: 18065.105 Da / Num. of mol.: 1 / Fragment: EPH RECEPTOR BINDING DOMAIN, RESIDUES 33-177 / Mutation: YES Source method: isolated from a genetically manipulated source Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE AT ASN 42 Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O43921 | ||
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | Q174N SITE-DIRECTED MUTATION TO PROMOTE CRYSTALLOG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 20% PEG 3350, 200 MM KNO3, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.81 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 10, 2007 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 18961 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 16 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KGY Resolution: 2.35→49.97 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.556 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.229 / 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: 42.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→49.97 Å
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Refine LS restraints |
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