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- PDB-1b0x: THE CRYSTAL STRUCTURE OF AN EPH RECEPTOR SAM DOMAIN REVEALS A MEC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1b0x | ||||||
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Title | THE CRYSTAL STRUCTURE OF AN EPH RECEPTOR SAM DOMAIN REVEALS A MECHANISM FOR MODULAR DIMERIZATION. | ||||||
![]() | PROTEIN (EPHA4 RECEPTOR TYROSINE KINASE) | ||||||
![]() | TRANSFERASE / RECEPTOR TYROSINE KINASE / PROTEIN INTERACTION MODULE / DIMERIZATION DOMAIN | ||||||
Function / homology | ![]() DH domain binding / EPH-Ephrin signaling / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / EPHA-mediated growth cone collapse / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / EPH-ephrin mediated repulsion of cells / neuron projection guidance ...DH domain binding / EPH-Ephrin signaling / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / EPHA-mediated growth cone collapse / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / EPH-ephrin mediated repulsion of cells / neuron projection guidance / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / regulation of synapse pruning / synapse pruning / 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 / regulation of dendritic spine morphogenesis / transmembrane-ephrin receptor activity / negative regulation of cell adhesion / negative regulation of epithelial to mesenchymal transition / adult walking behavior / motor neuron axon guidance / adherens junction organization / positive regulation of dendrite morphogenesis / positive regulation of amyloid-beta formation / regulation of axonogenesis / cochlea development / regulation of GTPase activity / positive regulation of protein tyrosine kinase activity / positive regulation of cell adhesion / negative regulation of long-term synaptic potentiation / ephrin receptor signaling pathway / axonal growth cone / axon terminus / positive regulation of JUN kinase activity / ephrin receptor binding / transmembrane receptor protein tyrosine kinase activity / negative regulation of cell migration / protein tyrosine kinase binding / dendritic shaft / filopodium / cell projection / adherens junction / 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 / negative regulation of neuron projection development / presynaptic membrane / early endosome membrane / cell body / postsynaptic membrane / perikaryon / mitochondrial outer membrane / protein autophosphorylation / dendritic spine / postsynaptic density / protein stabilization / cell adhesion / protein kinase activity / positive regulation of cell migration / axon / 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 | ![]() ![]() | ||||||
![]() | Stapleton, D. / Balan, I. / Pawson, T. / Sicheri, F. | ||||||
![]() | ![]() Title: The crystal structure of an Eph receptor SAM domain reveals a mechanism for modular dimerization. Authors: Stapleton, D. / Balan, I. / Pawson, T. / Sicheri, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 28.8 KB | Display | ![]() |
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PDB format | ![]() | 18.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363 KB | Display | ![]() |
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Full document | ![]() | 364.4 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 3.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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: 10265.485 Da / Num. of mol.: 1 / Fragment: SAM DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.66 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Details: OSMIC MULTILAYER OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 17787 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.04 |
Reflection | *PLUS Num. obs: 5663 / Observed criterion σ(I): -3 / Num. measured all: 17787 / Rmerge(I) obs: 0.004 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.01 |