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- PDB-2hel: Crystal structure of a mutant EphA4 kinase domain (Y742A) -

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Basic information

Entry
Database: PDB / ID: 2hel
TitleCrystal structure of a mutant EphA4 kinase domain (Y742A)
ComponentsEph receptor A4
KeywordsSIGNALING PROTEIN / TRANSFERASE / Tyr kinase / activation
Function / homology
Function and homology information


EPH-Ephrin signaling / DH domain binding / neuron projection fasciculation / : / EPHA-mediated growth cone collapse / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / EPH-ephrin mediated repulsion of cells / regulation of astrocyte differentiation / neuron projection guidance ...EPH-Ephrin signaling / DH domain binding / neuron projection fasciculation / : / EPHA-mediated growth cone collapse / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / EPH-ephrin mediated repulsion of cells / regulation of astrocyte differentiation / neuron projection guidance / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / glial cell migration / PH domain binding / regulation of modification of synaptic structure / regulation of synapse pruning / adherens junction organization / regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / innervation / adult walking behavior / regulation of GTPase activity / negative regulation of epithelial to mesenchymal transition / positive regulation of amyloid-beta formation / regulation of axonogenesis / positive regulation of intracellular signal transduction / negative regulation of long-term synaptic potentiation / cochlea development / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / ephrin receptor signaling pathway / axonal growth cone / ephrin receptor binding / axon terminus / transmembrane receptor protein tyrosine kinase activity / positive regulation of cell adhesion / axon guidance / protein tyrosine kinase binding / negative regulation of cell migration / dendritic shaft / adherens junction / filopodium / positive regulation of JNK cascade / peptidyl-tyrosine phosphorylation / receptor protein-tyrosine kinase / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / neuromuscular junction / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / negative regulation of neuron projection development / presynaptic membrane / protein autophosphorylation / early endosome membrane / perikaryon / dendritic spine / mitochondrial outer membrane / negative regulation of neuron apoptotic process / postsynaptic membrane / protein kinase activity / cell adhesion / protein stabilization / positive regulation of cell migration / axon / positive regulation of cell population proliferation / dendrite / glutamatergic synapse / cell surface / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain ...Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ephrin type-A receptor 4 / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWybenga-Groot, L.E. / Sicheri, F. / Pawson, T.
CitationJournal: EMBO J. / Year: 2006
Title: A change in conformational dynamics underlies the activation of Eph receptor tyrosine kinases.
Authors: Wiesner, S. / Wybenga-Groot, L.E. / Warner, N. / Lin, H. / Pawson, T. / Forman-Kay, J.D. / Sicheri, F.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eph receptor A4


Theoretical massNumber of molelcules
Total (without water)34,5771
Polymers34,5771
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.283, 101.081, 40.950
Angle α, β, γ (deg.)90.00, 108.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eph receptor A4


Mass: 34576.836 Da / Num. of mol.: 1 / Fragment: Juxtamembrane and Kinase domain / Mutation: Y604F, Y610F, Y742A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epha4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80VZ2, UniProt: Q03137*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% (w/v) PEG 8000, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 9232 / % possible obs: 88.6 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2478 666 6% of data, random
Rwork0.2087 --
all-10389 -
obs-9085 -
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 0 51 2018
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.96
X-RAY DIFFRACTIONc_bond_d0.006

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