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Yorodumi- PDB-4bka: crystal structure of the human EphA4 ectodomain in complex with h... -
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-Basic information
Entry | Database: PDB / ID: 4bka | ||||||
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Title | crystal structure of the human EphA4 ectodomain in complex with human ephrin A5 | ||||||
Components |
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Keywords | CELL ADHESION / CELL REPULSION / RECEPTOR CLUSTERING / RECEPTOR CIS INTERACTION / EPH-EPHRIN / EPH ECTODOMAIN / ERYTHROPOETIN-PRODUCING HEPATOCELLULAR RECEPTOR / LBD / SUSHI / EGF / FN | ||||||
Function / homology | Function and homology information neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / 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 / nephric duct morphogenesis ...neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / 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 / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / regulation of synapse pruning / synapse pruning / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cellular response to hypoxia / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of axon regeneration / glial cell migration / transmembrane-ephrin receptor activity / regulation of cell-cell adhesion / synaptic membrane adhesion / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / cellular response to follicle-stimulating hormone stimulus / collateral sprouting / positive regulation of collateral sprouting / regulation of insulin secretion involved in cellular response to glucose stimulus / transmembrane receptor protein tyrosine kinase activator activity / regulation of dendritic spine morphogenesis / chemorepellent activity / neurotrophin TRKA receptor binding / negative regulation of cell adhesion / negative regulation of epithelial to mesenchymal transition / regulation of cell morphogenesis / motor neuron axon guidance / adult walking behavior / positive regulation of synapse assembly / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Somitogenesis / regulation of focal adhesion assembly / positive regulation of amyloid-beta formation / regulation of axonogenesis / retinal ganglion cell axon guidance / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / positive regulation of protein tyrosine kinase activity / positive regulation of cell adhesion / negative regulation of long-term synaptic potentiation / basement membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / GABA-ergic synapse / axonal growth cone / regulation of microtubule cytoskeleton organization / axon terminus / cellular response to forskolin / ephrin receptor binding / protein tyrosine kinase binding / negative regulation of cell migration / filopodium / dendritic shaft / caveola / axon guidance / receptor protein-tyrosine kinase / regulation of actin cytoskeleton organization / adherens junction / postsynaptic density membrane / neuromuscular junction / peptidyl-tyrosine phosphorylation / Schaffer collateral - CA1 synapse / negative regulation of ERK1 and ERK2 cascade / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of neuron projection development / early endosome membrane / kinase activity / nervous system development / presynaptic membrane / amyloid-beta binding / protein tyrosine kinase activity / perikaryon / protein autophosphorylation / mitochondrial outer membrane / dendritic spine / protein stabilization / negative regulation of translation / cell adhesion / positive regulation of cell migration / protein kinase activity / positive regulation of protein phosphorylation / external side of plasma membrane / axon / positive regulation of cell population proliferation / glutamatergic synapse / dendrite Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.3 Å | ||||||
Authors | Seiradake, E. / Schaupp, A. / del Toro Ruiz, D. / Kaufmann, R. / Mitakidis, N. / Harlos, K. / Aricescu, A.R. / Klein, R. / Jones, E.Y. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Structurally Encoded Intraclass Differences in Epha Clusters Drive Distinct Cell Responses Authors: Seiradake, E. / Schaupp, A. / Del Toro Ruiz, D. / Kaufmann, R. / Mitakidis, N. / Harlos, K. / Aricescu, A.R. / Klein, R. / 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 | 4bka.cif.gz | 145.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bka.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bka_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 4bka_full_validation.pdf.gz | 473.6 KB | Display | |
Data in XML | 4bka_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 4bka_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bka ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bka | HTTPS FTP |
-Related structure data
Related structure data | 4bk4C 4bk5SC 4bkfC 4bkb 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 62649.336 Da / Num. of mol.: 1 / Fragment: HEPHA4 ECTODOMAIN, RESIDUES 20-547 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: 20689.596 Da / Num. of mol.: 1 Fragment: HEPHRINA5 RECEPTOR BINDING DOMAIN, RESIDUES 27-166 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: P52803 |
Sequence details | CONTAINS ARTIFICIAL N-TERMINAL SECRETION SIGNAL AND C- TERMINAL POLY-HISTIDINE TAG CONTAINS ...CONTAINS ARTIFICIAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 9.05 Å3/Da / Density % sol: 85.3 % / Description: NONE |
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Crystal grow | Details: 0.01 M MGSO4, 1.8 M LISO4, 0.05 M SODIUM CACODYLATE PH 6 AND ADDITIVE 4% BENZAMIDINE-HCL |
-Data collection
Diffraction |
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Diffraction source |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 4.95→48 Å / Num. obs: 11758 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.74 / Net I/σ(I): 3.32 | ||||||||||||||||||||
Reflection shell | Resolution: 4.95→5 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 0.32 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BK5 Resolution: 5.3→84.87 Å / Cor.coef. Fo:Fc: 0.727 / Cor.coef. Fo:Fc free: 0.684 / SU B: 0.008 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 1.588 / ESU R Free: 1.688 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY RIGID BODY AND TLS REFINEMENT WERE PERFORMED, NO INDIVIDUAL ATOM POSITIONS WERE REFINED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso mean: 243.358 Å2
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Refinement step | Cycle: LAST / Resolution: 5.3→84.87 Å
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LS refinement shell | Resolution: 5.3→5.438 Å / Total num. of bins used: 20
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