[English] 日本語
![](img/lk-miru.gif)
- PDB-4bk5: crystal structure of the human EphA4 ectodomain in complex with h... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4bk5 | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of the human EphA4 ectodomain in complex with human ephrin A5 (amine-methylated sample) | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / CELL ADHESION / CELL REPULSION / RECEPTOR CLUSTERING / RECEPTOR CIS INTERACTION / ERYTHROPOETIN-PRODUCING HEPATOCELLULAR RECEPTOR / LBD / EGF / FN | ||||||
Function / homology | ![]() 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 / 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 / regulation of dendritic spine morphogenesis / chemorepellent activity / neurotrophin TRKA receptor binding / transmembrane-ephrin receptor activity / negative regulation of cell adhesion / negative regulation of epithelial to mesenchymal transition / regulation of cell morphogenesis / adult walking behavior / motor neuron axon guidance / 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 / transmembrane receptor protein tyrosine kinase activator activity / 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 / GABA-ergic synapse / ephrin receptor signaling pathway / axonal growth cone / regulation of microtubule cytoskeleton organization / axon terminus / cellular response to forskolin / ephrin receptor binding / negative regulation of cell migration / protein tyrosine kinase binding / dendritic shaft / filopodium / caveola / regulation of actin cytoskeleton organization / 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 / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of neuron projection development / presynaptic membrane / kinase activity / nervous system development / 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 / positive regulation of protein phosphorylation / external side of plasma membrane / axon / glutamatergic synapse / dendrite / positive regulation of cell population proliferation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seiradake, E. / Schaupp, A. / del Toro Ruiz, D. / Kaufmann, R. / Mitakidis, N. / Harlos, K. / Aricescu, A.R. / Klein, R. / Jones, E.Y. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 275.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 225.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bk4SC ![]() 4bkaC ![]() 4bkfC ![]() 2x11S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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 Details: SAMPLE WAS AMINE-METHYLATED PRIOR TO CRYSTALLIZATION Source: (gene. exp.) ![]() ![]() References: UniProt: P54764, receptor protein-tyrosine kinase |
---|---|
#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 Details: SAMPLE WAS AMINE-METHYLATED PRIOR TO CRYSTALLIZATION Source: (gene. exp.) ![]() ![]() References: UniProt: P52803, receptor protein-tyrosine kinase |
Sequence details | SEQUENCE CORRESPONDS TO HEPHA4 RESIDUES 27-547 FUSED TO AN N-TERMINAL SECRETION SIGNAL SEQUENCE AND ...SEQUENCE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density % sol: 88.2 % Description: WE USED THE NEW CC CRITERIA TO DETERMINE THE HIGH RESOLUTION CUT-OFF. THE CC-HALF VALUE IN THE HIGHEST RES SHELL IS 15.9 |
---|---|
Crystal grow | Details: 8 % W-V POLYETHYLENE GLYCOL 8000 AND 0.1 M TRIS-HCL PH 8.5 |
-Data collection
Diffraction |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||
Detector |
| ||||||||||||||||||||
Radiation |
| ||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection | Resolution: 4→70 Å / Num. obs: 27221 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 130.48 Å2 / Rmerge(I) obs: 0.41 / Net I/σ(I): 7.7 | ||||||||||||||||||||
Reflection shell | Resolution: 4→4.05 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 0.59 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 4BK4, 2X11 Resolution: 4→70.41 Å / Cor.coef. Fo:Fc: 0.8006 / Cor.coef. Fo:Fc free: 0.8147 / SU R Cruickshank DPI: 1.078 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1 / SU Rfree Blow DPI: 0.537 / SU Rfree Cruickshank DPI: 0.555
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 187.97 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 1.707 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→70.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4→4.15 Å / Total num. of bins used: 14
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|