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- PDB-2qoo: Human EphA3 kinase and juxtamembrane region, Y596F:Y602F:Y742F tr... -

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Basic information

Entry
Database: PDB / ID: 2qoo
TitleHuman EphA3 kinase and juxtamembrane region, Y596F:Y602F:Y742F triple mutant
ComponentsEphrin receptor
KeywordsTRANSFERASE / receptor tyrosine kinase / juxtamembrane segment / structural genomics / mutant / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Phosphorylation / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


fasciculation of sensory neuron axon / fasciculation of motor neuron axon / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity ...fasciculation of sensory neuron axon / fasciculation of motor neuron axon / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to retinoic acid / axon guidance / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / cell migration / actin cytoskeleton / nuclear membrane / early endosome / cell adhesion / dendrite / extracellular region / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-A receptor 3, 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 3, 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 / 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 3 / receptor protein-tyrosine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsDavis, T. / Walker, J.R. / Newman, E.M. / Mackenzie, F. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Davis, T. / Walker, J.R. / Newman, E.M. / Mackenzie, F. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2008
Title: Autoregulation by the Juxtamembrane Region of the Human Ephrin Receptor Tyrosine Kinase A3 (EphA3).
Authors: Davis, T.L. / Walker, J.R. / Loppnau, P. / Butler-Cole, C. / Allali-Hassani, A. / Dhe-Paganon, S.
History
DepositionJul 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin receptor


Theoretical massNumber of molelcules
Total (without water)41,9161
Polymers41,9161
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.111, 38.255, 75.975
Angle α, β, γ (deg.)90.000, 102.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin receptor /


Mass: 41915.863 Da / Num. of mol.: 1
Fragment: Juxtamembrane segment and kinase domain: Residues 577-947
Mutation: Y596F, Y602F, Y742F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Placenta / Gene: EPHA3 / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6P4R6, UniProt: P29320*PLUS, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 1.83 Å3/Da / Density % sol: 32.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mg/mL Protein, 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→40 Å / Num. obs: 83007 / % possible obs: 98.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.035 / Χ2: 1.006 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.25-1.2930.6374391.00288.7
1.29-1.3540.50682910.98999
1.35-1.4140.34683190.99699.3
1.41-1.484.10.23283281.01399.4
1.48-1.574.10.15284271.04799.8
1.57-1.74.10.09483860.98399.9
1.7-1.874.10.0684020.978100
1.87-2.144.10.03984821.098100
2.14-2.694.10.02684740.954100
2.69-4040.02184590.99497.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GSF

2gsf


Resolution: 1.25→26.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.752 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 4138 5 %RANDOM
Rwork0.189 ---
obs0.19 82987 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.198 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 0 279 2571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222355
X-RAY DIFFRACTIONr_bond_other_d0.0010.021655
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9693206
X-RAY DIFFRACTIONr_angle_other_deg0.81134061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9015309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85523.942104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.08215446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7671517
X-RAY DIFFRACTIONr_chiral_restr0.0650.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022617
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
X-RAY DIFFRACTIONr_nbd_refined0.2060.2478
X-RAY DIFFRACTIONr_nbd_other0.1780.21781
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21220
X-RAY DIFFRACTIONr_nbtor_other0.0820.21166
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.229
X-RAY DIFFRACTIONr_mcbond_it0.8061.51903
X-RAY DIFFRACTIONr_mcbond_other0.1281.5575
X-RAY DIFFRACTIONr_mcangle_it0.93622351
X-RAY DIFFRACTIONr_scbond_it1.42331086
X-RAY DIFFRACTIONr_scangle_it1.874.5841
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 254 -
Rwork0.311 5089 -
all-5343 -
obs--86.01 %

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