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- PDB-7eed: Crystal structure of EphA7 mutant D751H -

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Basic information

Entry
Database: PDB / ID: 7eed
TitleCrystal structure of EphA7 mutant D751H
ComponentsEphrin type-A receptor 7
KeywordsMEMBRANE PROTEIN / Kinase domain / Mutant
Function / homology
Function and homology information


regulation of protein autophosphorylation / regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of synapse assembly / nephric duct morphogenesis / negative regulation of collateral sprouting / branching morphogenesis of a nerve / axon guidance receptor activity / regulation of cell-cell adhesion / GPI-linked ephrin receptor activity / chemorepellent activity ...regulation of protein autophosphorylation / regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of synapse assembly / nephric duct morphogenesis / negative regulation of collateral sprouting / branching morphogenesis of a nerve / axon guidance receptor activity / regulation of cell-cell adhesion / GPI-linked ephrin receptor activity / chemorepellent activity / transmembrane-ephrin receptor activity / EPH-Ephrin signaling / regulation of postsynapse organization / negative chemotaxis / retinal ganglion cell axon guidance / EPHA-mediated growth cone collapse / growth factor binding / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of peptidyl-tyrosine phosphorylation / regulation of ERK1 and ERK2 cascade / axon guidance / modulation of chemical synaptic transmission / brain development / receptor protein-tyrosine kinase / positive regulation of neuron apoptotic process / protein tyrosine kinase activity / neuron apoptotic process / positive regulation of protein phosphorylation / phosphorylation / glutamatergic synapse / dendrite / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 7, 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. ...Ephrin type-A receptor 7, 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 / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / 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 / 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
Similarity search - Domain/homology
Ephrin type-A receptor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsChakraborty, S. / Varma, A.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of clinically reported mutations Gly656Arg, Gly656Glu and Asp751His identified in the kinase domain of EphA7.
Authors: Chakraborty, S. / Varma, A.K.
History
DepositionMar 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 7


Theoretical massNumber of molelcules
Total (without water)34,4681
Polymers34,4681
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13790 Å2
Unit cell
Length a, b, c (Å)51.240, 51.240, 215.271
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ephrin type-A receptor 7 / EPH homology kinase 3 / EHK-3 / EPH-like kinase 11 / EK11 / hEK11


Mass: 34467.699 Da / Num. of mol.: 1 / Mutation: D751H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA7, EHK3, HEK11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15375, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Ammonium sulphate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54184 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3.05→71.76 Å / Num. obs: 5689 / % possible obs: 92.5 % / Redundancy: 1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.185 / Net I/σ(I): 11.2
Reflection shellResolution: 3.05→3.22 Å / Num. unique obs: 768 / CC1/2: 0.988

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2REI

2rei


Resolution: 3.05→44.375 Å / Cor.coef. Fo:Fc: 0.847 / Cor.coef. Fo:Fc free: 0.793 / SU B: 15.751 / SU ML: 0.298 / Cross valid method: FREE R-VALUE / ESU R Free: 0.504
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.247 255 4.529 %
Rwork0.1994 5376 -
all0.201 --
obs-5376 92.524 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.178 Å2
Baniso -1Baniso -2Baniso -3
1-0.526 Å20.263 Å20 Å2
2--0.526 Å2-0 Å2
3----1.705 Å2
Refinement stepCycle: LAST / Resolution: 3.05→44.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 0 6 2218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132262
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172157
X-RAY DIFFRACTIONr_angle_refined_deg1.681.643054
X-RAY DIFFRACTIONr_angle_other_deg1.1991.5814958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5845276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78421.27126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36315396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4861519
X-RAY DIFFRACTIONr_chiral_restr0.0650.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022547
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02535
X-RAY DIFFRACTIONr_nbd_refined0.230.2541
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22153
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21050
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1340.224
X-RAY DIFFRACTIONr_nbd_other0.2090.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2730.23
X-RAY DIFFRACTIONr_mcbond_it0.3582.9151110
X-RAY DIFFRACTIONr_mcbond_other0.3582.9141109
X-RAY DIFFRACTIONr_mcangle_it0.6914.3681384
X-RAY DIFFRACTIONr_mcangle_other0.694.371385
X-RAY DIFFRACTIONr_scbond_it0.0712.9241152
X-RAY DIFFRACTIONr_scbond_other0.0712.9251153
X-RAY DIFFRACTIONr_scangle_it0.2524.3791670
X-RAY DIFFRACTIONr_scangle_other0.2524.3811671
X-RAY DIFFRACTIONr_lrange_it2.26633.362540
X-RAY DIFFRACTIONr_lrange_other2.26533.3612541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.1290.243220.195375X-RAY DIFFRACTION90.8467
3.129-3.2140.239240.186335X-RAY DIFFRACTION79.4248
3.214-3.3070.199150.181355X-RAY DIFFRACTION88.9423
3.307-3.4080.199130.176327X-RAY DIFFRACTION79.2541
3.408-3.5190.282160.175329X-RAY DIFFRACTION92.246
3.519-3.6420.23670.156331X-RAY DIFFRACTION83.6634
3.642-3.7790.282160.181308X-RAY DIFFRACTION90.5028
3.779-3.9320.175100.166337X-RAY DIFFRACTION92.7808
3.932-4.1050.202130.144315X-RAY DIFFRACTION96.4706
4.105-4.3030.256240.143299X-RAY DIFFRACTION96.4179
4.303-4.5340.16120.148283X-RAY DIFFRACTION98.6622
4.534-4.8060.199110.151291X-RAY DIFFRACTION99.67
4.806-5.1330.24300.163256X-RAY DIFFRACTION100
5.133-5.5380.21450.185248X-RAY DIFFRACTION99.6063
5.538-6.0580.29890.192226X-RAY DIFFRACTION100
6.058-6.7570.24950.199219X-RAY DIFFRACTION100
6.757-7.7720.13460.198182X-RAY DIFFRACTION100
7.772-9.4470.27690.16156X-RAY DIFFRACTION100
9.447-13.0670.35862.19130X-RAY DIFFRACTION100
13.067-44.37526.51473X-RAY DIFFRACTION98.6842

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