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- PDB-3kul: Kinase domain of human ephrin type-A receptor 8 (EPHA8) -

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Basic information

Entry
Database: PDB / ID: 3kul
TitleKinase domain of human ephrin type-A receptor 8 (EPHA8)
Components(Ephrin type-A receptor ...) x 2
KeywordsTRANSFERASE / ATP-binding / kinase / nucleotide-binding / receptor / phosphorylation / transmembrane / tyrosine-protein kinase / Structural Genomics Consortium / SGC / Glycoprotein / Membrane / Phosphoprotein
Function / homology
Function and homology information


substrate-dependent cell migration / ephrin receptor activity / GPI-linked ephrin receptor activity / cellular response to follicle-stimulating hormone stimulus / transmembrane-ephrin receptor activity / EPH-Ephrin signaling / neuron remodeling / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin ...substrate-dependent cell migration / ephrin receptor activity / GPI-linked ephrin receptor activity / cellular response to follicle-stimulating hormone stimulus / transmembrane-ephrin receptor activity / EPH-Ephrin signaling / neuron remodeling / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of cell adhesion / axon guidance / receptor protein-tyrosine kinase / neuron projection development / early endosome membrane / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / neuron projection / phosphorylation / dendrite / ATP binding / plasma membrane
Similarity search - Function
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 ...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 / 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
BETA-MERCAPTOETHANOL / Ephrin type-A receptor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Kania, J. / Bountra, 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 8 (Epha8)
Authors: Walker, J.R. / Yermekbayeva, L. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-A receptor 8
B: Ephrin type-A receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9187
Polymers73,4772
Non-polymers4405
Water4,612256
1
A: Ephrin type-A receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0615
Polymers36,6991
Non-polymers3624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ephrin type-A receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8572
Polymers36,7791
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.140, 41.879, 145.815
Angle α, β, γ (deg.)90.00, 92.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Ephrin type-A receptor ... , 2 types, 2 molecules AB

#1: Protein Ephrin type-A receptor 8 / Tyrosine-protein kinase receptor EEK / EPH- and ELK-related kinase / HEK3


Mass: 36698.637 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 602-909)
Source method: isolated from a genetically manipulated source
Details: TYR at position 793 / Source: (gene. exp.) Homo sapiens (human) / Gene: EEK, EPHA8, HEK3, KIAA1459 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P29322, receptor protein-tyrosine kinase
#2: Protein Ephrin type-A receptor 8 / Tyrosine-protein kinase receptor EEK / EPH- and ELK-related kinase / HEK3


Mass: 36778.617 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 602-909)
Source method: isolated from a genetically manipulated source
Details: PTR at position 793 / Source: (gene. exp.) Homo sapiens (human) / Gene: EEK, EPHA8, HEK3, KIAA1459 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P29322, receptor protein-tyrosine kinase

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Non-polymers , 4 types, 261 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 32.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: WELL SOLUTION: 20% PEG 8000, 0.2 M NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 20 MG/ML, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 29557 / Num. obs: 29557 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rsym value: 0.116 / Net I/σ(I): 20.6
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.15 / Num. unique all: 1505 / Rsym value: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2REI

2rei


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.385 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.215 / 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
Rfree0.24389 1497 5.1 %RANDOM
Rwork0.1869 ---
obs0.18985 27960 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.62 Å2
2--0.84 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4221 0 24 256 4501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214364
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9575907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5715540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24822.132197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95715727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4751547
X-RAY DIFFRACTIONr_chiral_restr0.0890.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213307
X-RAY DIFFRACTIONr_mcbond_it0.5591.52687
X-RAY DIFFRACTIONr_mcangle_it1.05124328
X-RAY DIFFRACTIONr_scbond_it1.99631677
X-RAY DIFFRACTIONr_scangle_it3.064.51579
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 104 -
Rwork0.209 2103 -
obs--99.91 %
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)
15.93561.0271.95992.25850.78324.4693-0.03030.07550.1593-0.0343-0.0043-0.026-0.04010.03370.03460.06510.02360.01960.0279-0.01460.0736-16.580113.08271.8475
26.92686.6629-1.412410.1406-1.69883.20360.0014-0.031-0.2188-0.14840.0065-0.22630.09740.0145-0.0080.01740.01470.01260.1119-0.02990.0507-14.97548.407272.3695
32.80120.02080.32391.02070.12722.46780.02570.1720.3838-0.25590.03460.0231-0.43080.1394-0.06030.1894-0.00470.03980.13630.00320.1517-15.718318.830360.1982
42.2737-1.3519-0.46781.26040.04130.2127-0.073-0.14030.01220.0360.07560.0464-0.02150.0165-0.00260.08210.0138-0.00560.0836-0.01980.0676-8.09357.996864.2997
53.4854-1.19551.97213.2292-1.75383.06170.11040.0575-0.0253-0.2201-0.0690.19880.151-0.1091-0.04140.05520.00760.01730.0444-0.01570.0341-0.47473.131452.8367
64.583-1.83051.09116.1795-3.82115.38980.08380.2270.3-0.10220.07840.1768-0.3201-0.3026-0.16220.05790.03190.02320.0825-0.00120.0799-5.09588.399656.2113
78.92-13.6840.902317.14058.111534.04431.37370.9336-0.6407-0.1335-1.47651.94852.30290.18860.10281.1020.13280.14420.8499-0.01931.4003-7.312617.41238.8483
88.5699-1.27734.09781.304-2.56286.7336-0.2060.01870.44520.20110.1446-0.1455-0.6946-0.21380.06140.1860.03680.01870.04020.01470.13444.646520.734746.7253
91.6776-0.7130.72942.4943-1.7233.21830.0131-0.02040.10180.0336-0.1055-0.1853-0.0881-0.01290.09240.02730.01450.00810.01920.00050.03387.93610.278252.1107
102.75691.3450.79454.17672.06523.6179-0.03770.11540.0835-0.1491-0.085-0.2611-0.19070.15490.12270.04450.03320.01910.11450.04130.0816.250911.2748.3825
114.50841.70372.20644.02471.34748.289-0.16710.50180.0672-0.36470.00140.1443-0.41380.08590.16570.10810.0450.01230.11050.00750.0276.39589.658438.5869
122.9813-6.0727-0.369618.3291-5.13686.1780.10730.037-0.1215-0.191-0.2716-0.20960.64640.48290.16440.29470.0843-0.06970.1313-0.08220.10524.6248-5.644245.9643
136.4516-1.4178-4.5032.8881-0.401710.21480.02340.2237-0.11310.0278-0.01060.0623-0.0808-0.6176-0.01280.0838-0.0114-0.00330.1422-0.05910.1048-17.8092-9.0081.2809
147.97-2.0056-1.226113.55040.70394.7158-0.129-0.462-0.66570.8776-0.0621-0.64790.38260.51030.19110.12090.00120.0010.2299-0.01760.1578-4.9298-15.28392.014
157.6129-5.52422.296211.0144-4.50517.21810.18550.1804-0.0969-0.1423-0.11610.1452-0.0451-0.0127-0.06950.0311-0.01730.03030.1889-0.08380.0572-13.6302-7.03361.7266
164.7061.95730.4113.9340.95862.97640.13290.0132-0.65020.2696-0.09940.34460.7527-0.5136-0.03360.2473-0.0858-0.0010.21130.00350.258-12.6446-12.744116.6874
1718.806510.68549.954611.91536.805911.5241-0.1482-0.08180.3635-0.52430.0225-0.0882-0.4984-0.41310.12570.05020.02220.01910.1289-0.04450.077-13.5176-5.89629.9489
185.5842.39380.77562.4705-0.23061.23930.03070.2572-0.1857-0.0208-0.0744-0.0620.036-0.02120.04370.0940.01880.02020.1521-0.0380.01990.4854-4.92097.4717
193.40450.23220.18371.0513-0.87252.79090.00570.0047-0.07950.08020.0210.10550.0776-0.2418-0.02660.04820.00140.01860.0368-0.00960.0335-0.2314-2.783318.5096
208.77813.8668-0.84142.8337-3.19332.7032-0.1286-0.2361-0.22410.05860.0205-0.10760.0625-0.19930.10810.4496-0.05920.02160.4205-0.01160.359-4.1647-14.740130.5121
213.85060.8091-0.96551.3942-0.09212.64580.0261-0.1658-0.40890.1262-0.0291-0.14240.2343-0.0130.0030.0452-0.0098-0.00920.00870.0190.07888.5147-10.471924.7433
222.9034-3.10465.84999.2437-5.412711.43060.48320.5638-0.2536-0.4277-0.0646-0.15290.77451.1254-0.41860.23930.0605-0.03630.3365-0.12450.279118.6881-12.241416.5907
234.0054-0.4430.53145.95080.53632.45540.0686-0.1043-0.60390.0603-0.0476-0.29880.31180.2499-0.02090.0970.0239-0.01770.1570.04320.215719.3234-12.195325.1377
243.5998-0.49670.95364.9401-1.44284.5813-0.0972-0.2910.28570.0858-0.1148-0.2338-0.40680.08780.2120.0982-0.0283-0.02980.092-0.02220.035510.00050.726630.154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A627 - 644
2X-RAY DIFFRACTION2A645 - 662
3X-RAY DIFFRACTION3A663 - 691
4X-RAY DIFFRACTION4A692 - 729
5X-RAY DIFFRACTION5A730 - 763
6X-RAY DIFFRACTION6A764 - 786
7X-RAY DIFFRACTION7A791 - 796
8X-RAY DIFFRACTION8A800 - 814
9X-RAY DIFFRACTION9A815 - 839
10X-RAY DIFFRACTION10A840 - 872
11X-RAY DIFFRACTION11A873 - 884
12X-RAY DIFFRACTION12A885 - 900
13X-RAY DIFFRACTION13B627 - 638
14X-RAY DIFFRACTION14B639 - 653
15X-RAY DIFFRACTION15B654 - 672
16X-RAY DIFFRACTION16B673 - 696
17X-RAY DIFFRACTION17B697 - 703
18X-RAY DIFFRACTION18B704 - 735
19X-RAY DIFFRACTION19B736 - 781
20X-RAY DIFFRACTION20B782 - 801
21X-RAY DIFFRACTION21B802 - 834
22X-RAY DIFFRACTION22B835 - 841
23X-RAY DIFFRACTION23B842 - 864
24X-RAY DIFFRACTION24B865 - 899

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