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- PDB-8xpv: The Crystal Structure of EphA2 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xpv
TitleThe Crystal Structure of EphA2 from Biortus.
ComponentsEphrin type-A receptor 2
KeywordsTRANSFERASE / Host cell receptor for virus entry / Angiogenesis / ATP-binding
Function / homology
Function and homology information


notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / response to growth factor / activation of GTPase activity / tight junction / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / osteoclast differentiation / cell chemotaxis / molecular function activator activity / skeletal system development / protein localization to plasma membrane / cell motility / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / virus receptor activity / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 2, 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. ...Ephrin type-A receptor 2, 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 / Growth factor receptor cysteine-rich domain superfamily / 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 / 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
Chem-4Z5 / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of EphA2 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
History
DepositionJan 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2338
Polymers34,4061
Non-polymers8277
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.931, 107.504, 40.691
Angle α, β, γ (deg.)90.000, 108.686, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 34405.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Chemical ChemComp-4Z5 / 1-(3,3-dimethylbutyl)-3-{2-fluoro-4-methyl-5-[7-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-6-yl]phenyl}urea / LY3009120


Mass: 424.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29FN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium Acetate, 0.1M Sodium Cacodylate HCl pH6.5, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→38.576 Å / Num. obs: 37926 / % possible obs: 97.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.7
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.844 / Num. unique obs: 1845

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→38.576 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.53 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1903 1935 5.107 %
Rwork0.1641 35956 -
all0.165 --
obs-37891 97.69 %
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: 17.476 Å2
Baniso -1Baniso -2Baniso -3
1--0.541 Å2-0 Å2-0.257 Å2
2--1.073 Å2-0 Å2
3----0.292 Å2
Refinement stepCycle: LAST / Resolution: 1.55→38.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 57 251 2444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122314
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162276
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.6583129
X-RAY DIFFRACTIONr_angle_other_deg0.4051.5755241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.154523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71410422
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.7691098
X-RAY DIFFRACTIONr_chiral_restr0.0590.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02537
X-RAY DIFFRACTIONr_nbd_refined0.2060.2440
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.22034
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21136
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2158
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.216
X-RAY DIFFRACTIONr_nbd_other0.1860.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.221
X-RAY DIFFRACTIONr_mcbond_it1.1411.6731098
X-RAY DIFFRACTIONr_mcbond_other1.1361.6731098
X-RAY DIFFRACTIONr_mcangle_it1.9412.9851377
X-RAY DIFFRACTIONr_mcangle_other1.9412.9891378
X-RAY DIFFRACTIONr_scbond_it1.6841.9521216
X-RAY DIFFRACTIONr_scbond_other1.6831.9531217
X-RAY DIFFRACTIONr_scangle_it2.8193.4591743
X-RAY DIFFRACTIONr_scangle_other2.8193.461744
X-RAY DIFFRACTIONr_lrange_it5.09220.6322743
X-RAY DIFFRACTIONr_lrange_other4.80918.452670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.55-1.590.2921420.26825990.26928290.9460.95896.88940.246
1.59-1.6340.2691370.24625460.24728200.960.96595.14180.219
1.634-1.6810.2641430.22525170.22727150.9520.9797.97420.199
1.681-1.7330.2181330.20123720.20226400.970.97594.88640.177
1.733-1.7890.1811390.17523520.17525180.980.9898.92770.154
1.789-1.8520.1971220.17222640.17324830.9750.98196.09340.15
1.852-1.9220.1721120.16322170.16323840.9810.98397.6930.144
1.922-20.21040.16621480.16822880.9760.98398.42660.151
2-2.0890.18990.15820170.15921850.980.98696.84210.146
2.089-2.190.2031140.16119830.16321390.9770.98698.03650.15
2.19-2.3080.1981060.15618540.15819760.980.98699.19030.148
2.308-2.4480.181870.15717560.15818820.9830.98697.92770.151
2.448-2.6160.204840.15716850.1618000.9720.98598.27780.154
2.616-2.8250.169870.14615500.14716560.9810.98798.85270.145
2.825-3.0930.171870.14314390.14415410.9850.98899.02660.147
3.093-3.4550.165630.14112910.14213670.9820.98899.0490.15
3.455-3.9840.188670.13711670.1412430.9780.98899.27590.149
3.984-4.8660.175530.1399800.14110400.9840.98999.32690.155
4.866-6.8280.174350.1967770.1958130.9860.98499.8770.212
6.828-38.5760.151210.1884420.1864670.9850.9899.14350.213

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