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- PDB-2y6m: Crystal structure of EphA4 kinase domain -

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Basic information

Entry
Database: PDB / ID: 2y6m
TitleCrystal structure of EphA4 kinase domain
ComponentsEPHRIN TYPE-A RECEPTOR 4
KeywordsTRANSFERASE
Function / homology
Function and homology information


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 / 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 / glial cell migration / transmembrane-ephrin receptor activity / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / negative regulation of epithelial to mesenchymal transition / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / adult walking behavior / adherens junction organization / positive regulation of dendrite morphogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / cochlea development / regulation of GTPase activity / negative regulation of long-term synaptic potentiation / positive regulation of cell adhesion / ephrin receptor signaling pathway / positive regulation of protein tyrosine kinase activity / axon terminus / axonal growth cone / positive regulation of JUN kinase activity / protein tyrosine kinase binding / transmembrane receptor protein tyrosine kinase activity / ephrin receptor binding / negative regulation of cell migration / dendritic shaft / filopodium / cell projection / axon guidance / postsynaptic density membrane / adherens junction / Schaffer collateral - CA1 synapse / neuromuscular junction / 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 / presynaptic membrane / cell body / kinase activity / perikaryon / early endosome membrane / postsynaptic membrane / mitochondrial outer membrane / dendritic spine / protein autophosphorylation / 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
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 ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFarenc, C.J.A. / Celie, P.H.N. / Siegal, G.
CitationJournal: FEBS Lett. / Year: 2011
Title: Crystal Structure of the Epha4 Protein Tyrosine Kinase Domain in the Apo- and Dasatinib-Bound State.
Authors: Farenc, C.J.A. / Celie, P.H.N. / Tensen, C.P. / Siegal, G.
History
DepositionJan 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPHRIN TYPE-A RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2074
Polymers32,9311
Non-polymers2763
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.513, 91.045, 97.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EPHRIN TYPE-A RECEPTOR 4 / TYROSINE-PROTEIN KINASE RECEPTOR MPK-3 / TYROSINE-PROTEIN KINASE RECEPTOR SEK-1 / EPHA4


Mass: 32931.070 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 606-896
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET28AKDONLY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q03137, receptor protein-tyrosine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.21 Å3/Da / Density % sol: 44.26 % / Description: NONE
Crystal growDetails: AMMONIUM SULFATE, BIS TRIS PH5.5, PEG 10 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9779
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2010 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.7→30.85 Å / Num. obs: 31531 / % possible obs: 97.2 % / Observed criterion σ(I): 6 / Redundancy: 2.8 % / Biso Wilson estimate: 17.14 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HEL

2hel


Resolution: 1.7→30.851 Å / SU ML: 0.39 / σ(F): 1.36 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 1601 5.1 %
Rwork0.1749 --
obs0.1764 31500 95.94 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.294 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 18 281 2354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072206
X-RAY DIFFRACTIONf_angle_d0.9932989
X-RAY DIFFRACTIONf_dihedral_angle_d12.883855
X-RAY DIFFRACTIONf_chiral_restr0.072330
X-RAY DIFFRACTIONf_plane_restr0.004377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.75510.24621300.21142696X-RAY DIFFRACTION96
1.7551-1.81780.2291700.19552720X-RAY DIFFRACTION98
1.8178-1.89060.24321600.18672723X-RAY DIFFRACTION98
1.8906-1.97660.23351290.17742741X-RAY DIFFRACTION98
1.9766-2.08080.22571210.17542758X-RAY DIFFRACTION98
2.0808-2.21110.20441580.17832732X-RAY DIFFRACTION98
2.2111-2.38180.1981480.17442734X-RAY DIFFRACTION97
2.3818-2.62130.18721350.17122762X-RAY DIFFRACTION97
2.6213-3.00040.20681640.17122685X-RAY DIFFRACTION95
3.0004-3.77910.18331490.16352686X-RAY DIFFRACTION94
3.7791-30.85590.19561370.17472662X-RAY DIFFRACTION87

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