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- PDB-2rei: Kinase domain of human ephrin type-A receptor 7 (Epha7) -

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Basic information

Entry
Database: PDB / ID: 2rei
TitleKinase domain of human ephrin type-A receptor 7 (Epha7)
ComponentsEphrin type-A receptor 7
KeywordsTRANSFERASE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / PHOSPHORYLATION / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / ALTERNATIVE SPLICING / GLYCOPROTEIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / Polymorphism
Function / homology
Function and homology information


regulation of protein autophosphorylation / : / negative regulation of synapse assembly / branching morphogenesis of a nerve / nephric duct morphogenesis / negative regulation of collateral sprouting / axon guidance receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / chemorepellent activity ...regulation of protein autophosphorylation / : / negative regulation of synapse assembly / branching morphogenesis of a nerve / nephric duct morphogenesis / negative regulation of collateral sprouting / axon guidance receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / chemorepellent activity / EPH-Ephrin signaling / regulation of postsynapse organization / negative chemotaxis / retinal ganglion cell axon guidance / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell-cell adhesion / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / phosphorylation / regulation of peptidyl-tyrosine phosphorylation / regulation of ERK1 and ERK2 cascade / axon guidance / brain development / modulation of chemical synaptic transmission / receptor protein-tyrosine kinase / positive regulation of neuron apoptotic process / protein tyrosine kinase activity / neuron apoptotic process / positive regulation of protein 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 ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWalker, J.R. / Cuerrier, D. / Butler-Cole, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Kinase Domain of Human Ephrin Type-A Receptor 7 (Epha7).
Authors: Walker, J.R. / Cuerrier, D. / Butler-Cole, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionSep 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Ephrin type-A receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3582
Polymers36,2401
Non-polymers1181
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.880, 51.880, 215.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ephrin type-A receptor 7 / Tyrosine-protein kinase receptor EHK-3 / EPH homology kinase 3 / Receptor protein-tyrosine kinase HEK11


Mass: 36239.527 Da / Num. of mol.: 1 / Fragment: Kinase domain: Residues 590-899
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: EPHA7, EHK3, HEK11 / Plasmid: pNIC-CH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q15375, receptor protein-tyrosine kinase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Well solution: 20% PEG 3350, 0.2 M NH4 formate, 0.1 M HEPES pH 7.0. Protein solution: 12 mg/mL. Drops: 1:1 ratio of well:protein solution. Crystals cryoprotected by transfer to drop ...Details: Well solution: 20% PEG 3350, 0.2 M NH4 formate, 0.1 M HEPES pH 7.0. Protein solution: 12 mg/mL. Drops: 1:1 ratio of well:protein solution. Crystals cryoprotected by transfer to drop containing mother liquor to which MPD was added to 25%, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL SI(111), SAGITALLY FOCUSING CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→45 Å / Num. obs: 43283 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rsym value: 0.065 / Net I/σ(I): 41.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.52 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GSF

2gsf


Resolution: 1.6→44.95 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.713 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.18678 2171 5 %RANDOM
Rwork0.16255 ---
obs0.1637 40895 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.703 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 0 300 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222313
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9533143
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2475294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12123.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46215394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2031518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21154
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21613
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6741.51477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04722318
X-RAY DIFFRACTIONr_scbond_it1.9443959
X-RAY DIFFRACTIONr_scangle_it3.0494.5825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 171 -
Rwork0.197 3021 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
141.598420.9754-11.264810.72-6.722110.61881.4574-1.65410.71241.3622-0.9334-0.6725-1.03330.7184-0.5240.15030.0167-0.10780.4865-0.08790.244425.390612.24096.6326
24.3291-0.46782.46182.5388-0.417117.8269-0.103-0.5832-0.17620.04780.0315-0.02050.329-0.39970.0715-0.18670.0154-0.0157-0.0198-0.0187-0.075433.109510.269-8.5901
310.5939-4.5929-0.67139.79744.26276.8222-0.05760.21670.2419-0.3801-0.18930.1464-0.357-0.41390.2469-0.1646-0.02330.0099-0.0222-0.0144-0.093925.630813.4401-18.6706
43.4050.70630.64661.2327-0.69665.0415-0.0894-0.39070.37740.2139-0.03530.0592-0.5645-0.29410.1247-0.11010.042-0.02370.0464-0.0694-0.030125.969316.5293-7.3815
52.68630.59430.10980.4383-0.04910.115-0.07130.2675-0.1293-0.08790.0873-0.05040.03250.095-0.016-0.13290.02920.0033-0.0277-0.0265-0.139614.28996.5402-14.2171
64.427-1.577-0.22221.6264-0.06344.0771-0.0892-0.05720.13080.02220.1256-0.1814-0.1590.3618-0.0364-0.1921-0.0098-0.0003-0.03950.0004-0.148910.7768.6083-5.6514
71.9298-0.42020.70951.62140.34163.2324-0.1163-0.01670.1263-0.01430.04420.0346-0.26170.03840.0721-0.20170.00410.001-0.13560.0077-0.1586-0.803713.2976-3.63
814.10619.7791-6.673516.8088-10.037413.019-0.1023-0.38010.80920.6938-0.05660.0499-1.0583-0.30790.159-0.06350.0761-0.082-0.0589-0.0661-0.0605-8.608721.26150.6449
93.4844-1.47980.86642.2616-0.57952.03910.0041-0.2229-0.4430.00610.01960.20070.2921-0.1374-0.0236-0.1648-0.00510.0105-0.10080.0393-0.0981-5.01312.4753-3.0417
109.5966-15.5466-3.173926.85445.63041.1928-0.58280.367-0.35830.38960.78151.64551.0426-1.3451-0.19870.31330.0118-0.08760.16340.0450.36-7.9606-9.5426-11.6096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA607 - 61919 - 31
2X-RAY DIFFRACTION2AA620 - 63432 - 46
3X-RAY DIFFRACTION3AA635 - 65747 - 69
4X-RAY DIFFRACTION4AA658 - 68870 - 100
5X-RAY DIFFRACTION5AA689 - 745101 - 157
6X-RAY DIFFRACTION6AA746 - 802158 - 214
7X-RAY DIFFRACTION7AA803 - 841215 - 253
8X-RAY DIFFRACTION8AA842 - 851254 - 263
9X-RAY DIFFRACTION9AA852 - 894264 - 306
10X-RAY DIFFRACTION10AA895 - 902307 - 314

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