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- PDB-7eec: Crystal structure of EphA7 mutant G656R -

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Basic information

Entry
Database: PDB / ID: 7eec
TitleCrystal structure of EphA7 mutant G656R
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: 3.1 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)34,6831
Polymers34,6831
Non-polymers00
Water905
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 area13930 Å2
Unit cell
Length a, b, c (Å)51.780, 51.780, 216.080
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: 34682.926 Da / Num. of mol.: 1 / Mutation: G656R
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.: 5 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
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: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3.1→72.03 Å / Num. obs: 5944 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 0.984 / Rmerge(I) obs: 0.175 / Net I/σ(I): 11.9
Reflection shellResolution: 3.1→3.27 Å / Rmerge(I) obs: 0.175 / Num. unique obs: 874

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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: 3.1→44.8428 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.893 / SU B: 16.647 / SU ML: 0.294 / Cross valid method: FREE R-VALUE / ESU R Free: 0.415
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2101 294 4.946 %
Rwork0.1813 5650 -
all0.183 --
obs-5944 100 %
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: 32.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.056 Å20.028 Å20 Å2
2--0.056 Å2-0 Å2
3----0.182 Å2
Refinement stepCycle: LAST / Resolution: 3.1→44.8428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 0 5 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132267
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172165
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6413062
X-RAY DIFFRACTIONr_angle_other_deg1.2091.5824976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8875277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46321.172128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95615399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3551520
X-RAY DIFFRACTIONr_chiral_restr0.0620.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02539
X-RAY DIFFRACTIONr_nbd_refined0.2250.2550
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.22096
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21082
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.222
X-RAY DIFFRACTIONr_nbd_other0.2190.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3220.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_mcbond_it0.0813.431111
X-RAY DIFFRACTIONr_mcbond_other0.0813.431110
X-RAY DIFFRACTIONr_mcangle_it0.1575.1431387
X-RAY DIFFRACTIONr_mcangle_other0.1575.1441388
X-RAY DIFFRACTIONr_scbond_it0.0123.4361156
X-RAY DIFFRACTIONr_scbond_other0.0123.4371157
X-RAY DIFFRACTIONr_scangle_it0.0545.1541675
X-RAY DIFFRACTIONr_scangle_other0.0545.1551676
X-RAY DIFFRACTIONr_lrange_it0.90139.4612572
X-RAY DIFFRACTIONr_lrange_other0.90139.4582573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.233280.223409X-RAY DIFFRACTION100
3.18-3.2670.23210.22408X-RAY DIFFRACTION100
3.267-3.3610.229250.214377X-RAY DIFFRACTION100
3.361-3.4640.23220.196404X-RAY DIFFRACTION100
3.464-3.5770.233150.193353X-RAY DIFFRACTION100
3.577-3.7020.16130.18396X-RAY DIFFRACTION100
3.702-3.840.27160.184314X-RAY DIFFRACTION100
3.84-3.9960.096210.187347X-RAY DIFFRACTION100
3.996-4.1720.22180.161302X-RAY DIFFRACTION100
4.172-4.3740.24140.167311X-RAY DIFFRACTION100
4.374-4.6080.22540.161306X-RAY DIFFRACTION100
4.608-4.8840.184150.169269X-RAY DIFFRACTION100
4.884-5.2170.129100.177277X-RAY DIFFRACTION100
5.217-5.6290.203130.201234X-RAY DIFFRACTION100
5.629-6.1560.29200.186210X-RAY DIFFRACTION100
6.156-6.8670.278190.181199X-RAY DIFFRACTION100
6.867-7.8980.10910.143182X-RAY DIFFRACTION100
7.898-9.5990.168140.124148X-RAY DIFFRACTION100
9.599-13.2750.31720.139131X-RAY DIFFRACTION100

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