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- PDB-3ckh: Crystal structure of Eph A4 receptor -

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Basic information

Entry
Database: PDB / ID: 3ckh
TitleCrystal structure of Eph A4 receptor
ComponentsEphrin type-A receptor 4
KeywordsTRANSFERASE / Eph receptor / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


DH domain binding / positive regulation of Rho guanyl-nucleotide exchange factor activity / neuron projection fasciculation / 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 ...DH domain binding / positive regulation of Rho guanyl-nucleotide exchange factor activity / neuron projection fasciculation / 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 axon regeneration / transmembrane-ephrin receptor activity / glial cell migration / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / adult walking behavior / negative regulation of epithelial to mesenchymal transition / Somitogenesis / positive regulation of amyloid-beta formation / regulation of GTPase activity / regulation of axonogenesis / EPHA-mediated growth cone collapse / cochlea development / positive regulation of protein tyrosine kinase activity / negative regulation of long-term synaptic potentiation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / axonal growth cone / axon terminus / ephrin receptor binding / positive regulation of cell adhesion / protein tyrosine kinase binding / negative regulation of cell migration / filopodium / dendritic shaft / axon guidance / adherens junction / postsynaptic density membrane / neuromuscular junction / receptor protein-tyrosine kinase / Schaffer collateral - CA1 synapse / negative regulation of ERK1 and ERK2 cascade / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / negative regulation of neuron projection development / kinase activity / presynaptic membrane / amyloid-beta binding / early endosome membrane / protein tyrosine kinase activity / perikaryon / mitochondrial outer membrane / protein autophosphorylation / dendritic spine / negative regulation of translation / 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 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) / Galactose-binding domain-like / 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 / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsShi, J.H. / Song, J.X.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure and NMR Binding Reveal That Two Small Molecule Antagonists Target the High Affinity Ephrin-binding Channel of the EphA4 Receptor.
Authors: Qin, H. / Shi, J. / Noberini, R. / Pasquale, E.B. / Song, J.
History
DepositionMar 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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 1.3Apr 13, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 4
B: Ephrin type-A receptor 4


Theoretical massNumber of molelcules
Total (without water)41,6912
Polymers41,6912
Non-polymers00
Water2,576143
1
A: Ephrin type-A receptor 4


Theoretical massNumber of molelcules
Total (without water)20,8461
Polymers20,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin type-A receptor 4


Theoretical massNumber of molelcules
Total (without water)20,8461
Polymers20,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ephrin type-A receptor 4

B: Ephrin type-A receptor 4


Theoretical massNumber of molelcules
Total (without water)41,6912
Polymers41,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area1330 Å2
ΔGint-8.2 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.749, 71.121, 127.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Ephrin type-A receptor 4 / Tyrosine-protein kinase receptor SEK / Receptor protein-tyrosine kinase HEK8 / Tyrosine-protein kinase TYRO1


Mass: 20845.625 Da / Num. of mol.: 2 / Fragment: UNP residues 29-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA4, HEK8, SEK, TYRO1 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami (DE3)
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 16% isopropanol, 0.1M Hepes, pH7.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→63.51 Å / Num. obs: 21938 / % possible obs: 98 % / Redundancy: 7.19 % / Rmerge(I) obs: 0.102 / Χ2: 1 / Net I/σ(I): 8.2 / Scaling rejects: 1192
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.3-2.385.210.5632.1974918700.8685.3
2.38-2.486.620.5482.51413221310.997.1
2.48-2.597.670.5332.81682621920.89100
2.59-2.737.710.47931694121980.91100
2.73-2.97.750.4183.61711022060.98100
2.9-3.127.770.3274.41733922211.0499.9
3.12-3.447.70.2036.31735322341.0999.8
3.44-3.937.470.1319.81700822351.1899.8
3.93-4.956.90.07117.61582522571.0798.6
4.95-63.516.790.04827.71659823940.9799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å40.63 Å
Translation2.5 Å40.63 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9LDzdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NUK, 2BBA

1nuk

2bba


Resolution: 2.8→19.71 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1126 9.11 %RANDOM
Rwork0.228 ---
obs0.234 12355 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 43.47 Å2 / Biso mean: 71.9 Å2 / Biso min: 151.41 Å2
Baniso -1Baniso -2Baniso -3
1-35.958 Å2-0 Å2-0 Å2
2---20.169 Å20 Å2
3----16.326 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 0 143 2824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072733
X-RAY DIFFRACTIONf_angle_d1.1713696
X-RAY DIFFRACTIONf_chiral_restr0.074414
X-RAY DIFFRACTIONf_plane_restr0.008475
X-RAY DIFFRACTIONf_dihedral_angle_d20.124970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.9270.3711380.3051371150999
2.927-3.0810.3791370.2661381151899
3.081-3.2730.3241370.2361376151399
3.273-3.5240.3141410.2211396153799
3.524-3.8770.3111410.221398153999
3.877-4.4320.2791400.1981398153898
4.432-5.5630.2191400.1771398153897
5.563-19.710.2671520.241511166399

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