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- PDB-2gsf: The Human Epha3 Receptor Tyrosine Kinase and Juxtamembrane Region -

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Basic information

Entry
Database: PDB / ID: 2gsf
TitleThe Human Epha3 Receptor Tyrosine Kinase and Juxtamembrane Region
ComponentsEphrin type-A receptor 3
KeywordsTRANSFERASE / ATP-binding / Kinase / Membrane / Nucleotide-binding / Phosphorylation / Receptor / Transmembrane / Tyrosine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


fasciculation of sensory neuron axon / fasciculation of motor neuron axon / ephrin receptor activity / regulation of epithelial to mesenchymal transition / GPI-linked ephrin receptor activity / transmembrane-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 / ephrin receptor activity / regulation of epithelial to mesenchymal transition / GPI-linked ephrin receptor activity / transmembrane-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 / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / axon guidance / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.77 Å
AuthorsWalker, J.R. / Davis, T. / Dong, A. / Newman, E.M. / MacKenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Walker, J.R. / Davis, T. / Dong, A. / Newman, E.M. / MacKenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure Of The Human Epha3 Receptor Tyrosine Kinase and Juxtamembrane Region
Authors: Davis, T. / Walker, J.R. / Dong, A. / Newman, E.M. / MacKenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionApr 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The sequence is in accordance with the reference Chiari et al., 2000, Cancer Res., 60, 4855-4863

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 3


Theoretical massNumber of molelcules
Total (without water)41,9641
Polymers41,9641
Non-polymers00
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.163, 38.274, 76.333
Angle α, β, γ (deg.)90.00, 102.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin type-A receptor 3 / Tyrosine-protein kinase receptor ETK1 / HEK / HEK4


Mass: 41963.863 Da / Num. of mol.: 1
Fragment: Catalytic Domain, Juxtamembrane Region, residues 577-947
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA3, ETK, ETK1, HEK / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli)
References: UniProt: P29320, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.84 Å3/Da / Density % sol: 33.23 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 20 mg/mL protein, 25% PEG 3350, 0.2M Ammonium Sulfate, 0.1M Hepes, 20% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 29945 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 48.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 21.6 / % possible all: 64.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→19.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.596 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19455 1513 5.1 %RANDOM
Rwork0.15805 ---
obs0.15996 28392 99.12 %-
all-29945 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-1.24 Å2
2---0.01 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.77→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 0 264 2497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222277
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9673073
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0895277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04323.73799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62515415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9891516
X-RAY DIFFRACTIONr_chiral_restr0.110.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021679
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21131
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21602
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.76131443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.57342259
X-RAY DIFFRACTIONr_scbond_it3.4875965
X-RAY DIFFRACTIONr_scangle_it5.0967814
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 113 -
Rwork0.156 2026 -
obs--96.79 %
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)
137.9848.27475.88815.3053.03961.794-0.0268-2.66560.75930.468-0.70391.12460.2506-0.49920.7307-0.0199-0.010.0656-0.0027-0.09660.1051-11.696727.475651.7155
23.5886-0.41241.95797.94743.23412.5828-0.0606-0.20670.0645-0.1637-0.0930.4442-0.1669-0.18970.1536-0.01820.017-0.00390.06640.0080.0707-22.445213.044941.8963
33.29540.67141.798622.223822.83728.6398-0.0248-0.353-0.34661.11630.4876-0.65751.40440.3149-0.46280.0136-0.0117-0.01070.04470.0997-0.003-17.37314.32755.1079
42.1152-0.66661.47141.7809-0.73887.28020.0528-0.1257-0.1003-0.02160.09080.07950.12860.0034-0.14360.0283-0.005-0.00490.03330.00670.0721-16.65098.180639.8354
510.32886.1678-4.84664.841-3.04712.29440.3758-0.68780.43870.2611-0.26140.2704-0.13240.1243-0.1144-0.0095-0.0440.00540.0957-0.05920.0083-18.802717.950557.4287
64.48660.3562-0.63690.82060.07511.77430.0012-0.05520.0389-0.0283-0.02560.1507-0.076-0.20010.02440.02120.0140.00140.0293-0.00650.0501-13.756315.685946.6744
73.5293-2.69231.96414.0391-2.01491.22750.1545-0.0549-0.1237-0.0658-0.03720.19780.169-0.0611-0.11730.0376-0.0025-0.00350.01890.00530.055-1.16950.059851.3146
80.9004-0.71310.16983.911-0.01330.80440.04060.0437-0.0141-0.075-0.0397-0.0502-0.02860.0243-0.00090.0337-0.0107-0.0020.04190.00350.03046.906111.286348.7399
91.03210.84681.262413.19282.49021.71340.0076-0.16710.06830.5141-0.08050.36720.0502-0.1580.0730.0266-0.00650.01780.0379-0.010.0207-0.327614.111858.5797
101.7089-0.16260.72252.0847-0.4462.57160.0045-0.3290.14870.19440.03890.1849-0.3087-0.2874-0.04340.05420.01840.02320.0645-0.02830.0584-2.077612.600853.6126
110.588-0.22010.25881.65310.51961.2328-0.0115-0.11780.03180.0836-0.02660.0406-0.0735-0.08730.03810.0228-0.00180.00280.0513-0.00820.01177.335514.921562.6778
122.58681.48572.58344.72721.54818.15810.0374-0.1811-0.03770.2982-0.17730.19220.1253-0.1820.13990.0297-0.01840.01510.04840.01960.0237.0375.536971.361
131.270.07120.02241.3261-0.73972.2270.0399-0.07670.02640.1265-0.1116-0.1012-0.07220.11780.07170.0262-0.0254-0.01270.06870.00560.033616.751513.041763.423
143.8342-3.0023-1.19475.02991.19133.3381-0.07040.1756-0.0662-0.07120.0309-0.26370.10360.29090.03950.0202-0.02980.02180.1144-0.00220.073818.651311.751147.6904
1524.60030.26833.919921.5685-2.083719.60040.33540.1934-1.0956-0.6969-0.0966-0.6091.11060.8117-0.23880.04580.0213-0.03080.10450.02130.005818.93544.374969.2702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA595 - 61221 - 38
2X-RAY DIFFRACTION2AA613 - 62339 - 49
3X-RAY DIFFRACTION3AA624 - 63450 - 60
4X-RAY DIFFRACTION4AA635 - 65361 - 79
5X-RAY DIFFRACTION5AA654 - 67680 - 102
6X-RAY DIFFRACTION6AA677 - 700103 - 126
7X-RAY DIFFRACTION7AA701 - 714127 - 140
8X-RAY DIFFRACTION8AA715 - 742141 - 168
9X-RAY DIFFRACTION9AA743 - 752169 - 178
10X-RAY DIFFRACTION10AA753 - 788179 - 214
11X-RAY DIFFRACTION11AA789 - 821215 - 247
12X-RAY DIFFRACTION12AA822 - 833248 - 259
13X-RAY DIFFRACTION13AA834 - 869260 - 295
14X-RAY DIFFRACTION14AA870 - 893296 - 319
15X-RAY DIFFRACTION15AA899 - 904325 - 330

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