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- PDB-3c8x: Crystal structure of the ligand binding domain of human Ephrin A2... -

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Basic information

Entry
Database: PDB / ID: 3c8x
TitleCrystal structure of the ligand binding domain of human Ephrin A2 (Epha2) receptor protein kinase
ComponentsEphrin type-A receptor 2
KeywordsTRANSFERASE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / PHOSPHORYLATION / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / GLYCOPROTEIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / Phosphoprotein
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 / regulation of blood vessel endothelial cell migration / leading edge membrane ...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 / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / response to growth factor / bone remodeling / positive regulation of bicellular tight junction assembly / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / tight junction / RND1 GTPase cycle / neural tube development / 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 / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / transmembrane receptor protein tyrosine kinase activity / RAC1 GTPase cycle / osteoclast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / molecular function activator activity / protein localization to plasma membrane / skeletal system development / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / neuron differentiation / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / defense response to Gram-positive bacterium / cell adhesion / 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) / Galactose-binding domain-like / 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 / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWalker, J.R. / Yermekbayeva, L. / Seitova, A. / Butler-Cole, C. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Architecture of Eph receptor clusters.
Authors: Himanen, J.P. / Yermekbayeva, L. / Janes, P.W. / Walker, J.R. / Xu, K. / Atapattu, L. / Rajashankar, K.R. / Mensinga, A. / Lackmann, M. / Nikolov, D.B. / Dhe-Paganon, S.
History
DepositionFeb 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)23,5691
Polymers23,5691
Non-polymers00
Water1,982110
1
A: Ephrin type-A receptor 2

A: Ephrin type-A receptor 2


Theoretical massNumber of molelcules
Total (without water)47,1372
Polymers47,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.518, 92.518, 41.291
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 23568.516 Da / Num. of mol.: 1 / Fragment: Ligand binding domain: Residues 23-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK
Plasmid details: Plasmid transfer vector pFHMSP-LIC-N containing the gene was transformed into DH10Bac E.coli cells (Invitrogen) to obtain recombinant viral DNA. SF9 cells were transfected with ...Plasmid details: Plasmid transfer vector pFHMSP-LIC-N containing the gene was transformed into DH10Bac E.coli cells (Invitrogen) to obtain recombinant viral DNA. SF9 cells were transfected with Bacmid DNA using Cellfectin reagent (Invitrogen), and recombinant baculovirus was generated. Viral stock was amplified from P1 to P3.
Plasmid: pFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE CORRECT SEQUENCE IS PROVIDED IN GENBANK ENTRY NP_004422.

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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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: AN IN-SITU PROTEOLYSIS STRATEGY WAS USED TO GENERATE HIGH QUALITY CRYSTALS. TRYPSIN WAS ADDED FROM A 1.5 GRAM/L STOCK TO A PROTEIN SAMPLE (AT 6.2 GRAM/L) TO A FINAL TRYPSIN CONC OF 6.2 ...Details: AN IN-SITU PROTEOLYSIS STRATEGY WAS USED TO GENERATE HIGH QUALITY CRYSTALS. TRYPSIN WAS ADDED FROM A 1.5 GRAM/L STOCK TO A PROTEIN SAMPLE (AT 6.2 GRAM/L) TO A FINAL TRYPSIN CONC OF 6.2 MICROGRAM/L BEFORE CRYSTAL PLATES WERE SET AT 291.2K. 25% PEG 3350, 0.1 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5. PARATONE-N WAS USED AS THE CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 11, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. all: 14975 / Num. obs: 14975 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rsym value: 0.151 / Net I/σ(I): 15.44
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.8281 / Num. unique all: 1453 / Rsym value: 0.849 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KGY

1kgy


Resolution: 1.95→35 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.795 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.141 / 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
Rfree0.22623 755 5 %RANDOM
Rwork0.16291 ---
obs0.16583 14205 99.8 %-
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: 24.222 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å20 Å2
2--1.44 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 0 110 1390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_angle_refined_deg1.52
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.83
X-RAY DIFFRACTIONr_chiral_restr0.113
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_nbd_refined0.197
X-RAY DIFFRACTIONr_nbtor_refined0.312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.195
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.193
X-RAY DIFFRACTIONr_mcbond_it1.953
X-RAY DIFFRACTIONr_mcangle_it2.758
X-RAY DIFFRACTIONr_scbond_it3.616
X-RAY DIFFRACTIONr_scangle_it4.785
LS refinement shellResolution: 1.95→2.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 55 -
Rwork0.23 995 -
obs--97.31 %
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)
18.339-2.62954.653115.4705-3.61078.47060.1543-0.03680.16660.0598-0.29480.4468-0.2184-0.38490.14050.0963-0.0051-0.01230.1948-0.01920.1449-23.944660.2669-9.3906
2108.38585.845865.676.44230.541141.25861.81844.945-3.5701-0.7725-0.0048-0.19371.64092.6092-1.81360.1282-0.0366-0.05210.3272-0.10830.082-19.849550.4624-4.0723
39.8478-4.15222.304310.906110.077413.87320.12760.59870.13151.21210.02270.01250.34060.9576-0.15030.122-0.03290.00510.2717-0.00270.1532-9.826248.64346.5525
44.75732.39593.54341.25942.00443.55520.17130.1299-0.53630.08010.001-0.18920.33720.1762-0.17230.0932-0.01070.01270.1467-0.03130.1843-20.169145.61586.2616
52.92611.92243.08161.8952.7534.1372-0.10770.169-0.1654-0.15120.1192-0.06050.03930.2242-0.01150.1304-0.04520.01280.14250.00080.1478-24.707546.38053.9839
62.4460.1334-0.99212.5776-1.6044.6554-0.0563-0.1342-0.01450.0146-0.0114-0.1022-0.1560.29130.06770.1103-0.00280.00370.2252-0.0040.1937-11.68755.35327.5449
73.5115-0.4469-2.27482.7622-0.31275.68310.15340.34950.3588-0.1594-0.00180.0877-0.41320.0601-0.15150.139-0.0484-0.02450.14410.02290.172-17.949566.1046-8.4842
80.7793-1.03571.70731.6456-2.982910.89320.0695-0.221-0.00860.07680.14320.07640.1279-0.2805-0.21270.1017-0.0214-0.00230.1647-0.00770.1509-27.237657.847913.242
90.95161.84633.64443.58227.070913.95710.0083-0.1376-0.34830.8266-0.30260.00180.56590.05790.29430.1129-0.03070.04810.1684-0.00130.1488-25.654.632826.149
1016.1951-6.377619.06564.7342-8.267526.9744-0.03240.03830.26250.16110.01650.0133-0.36340.28220.01580.1123-0.01540.02410.2437-0.01650.1205-19.387559.684121.8602
113.5796-0.6013-3.74250.8747-0.49765.5522-0.0880.17670.1632-0.1195-0.0207-0.05370.03620.15440.10870.1404-0.04840.00010.17270.01450.1346-10.877362.6838-0.2812
1215.38099.7387-1.32398.56067.010325.8402-0.52530.11540.3599-0.0734-0.0173-0.0560.34730.65040.54260.01560.0365-0.0430.22610.13180.1421-3.996553.8575-1.8502
1313.4771-3.3716-5.728412.2554-5.29776.4046-0.1771-0.7344-0.0633-0.3232-0.0527-1.2946-0.19060.84520.22980.0448-0.0895-0.0280.2021-0.00460.1491-5.395662.79513.888
147.12262.5163.193818.4681-11.200610.07860.4346-0.78170.81340.75640.52821.4899-0.8279-0.5615-0.96280.1502-0.03140.09850.1664-0.01130.2424-20.717767.40639.0186
153.68840.2592-2.14551.1676-1.82495.45630.00860.21420.19920.17220.0290.0092-0.4123-0.1196-0.03760.185-0.0671-0.02240.1416-0.03810.1811-20.80865.40680.6546
160.8634-0.19190.04640.7844-0.65670.5659-0.0008-0.00320.0452-0.04-0.0689-0.0576-0.0020.12660.06970.1146-0.0389-0.00860.16750.00480.1381-15.464158.70555.3521
171.57580.8606-2.44594.0305-4.386612.0422-0.07840.33170.1242-0.60030.24390.29390.3229-0.292-0.16550.0814-0.0269-0.01820.19370.03040.1966-24.206562.7668-5.9103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 3431 - 38
2X-RAY DIFFRACTION2AA35 - 4339 - 47
3X-RAY DIFFRACTION3AA44 - 4948 - 53
4X-RAY DIFFRACTION4AA50 - 5854 - 62
5X-RAY DIFFRACTION5AA59 - 7263 - 76
6X-RAY DIFFRACTION6AA73 - 8577 - 89
7X-RAY DIFFRACTION7AA86 - 9890 - 102
8X-RAY DIFFRACTION8AA99 - 105103 - 109
9X-RAY DIFFRACTION9AA106 - 111110 - 115
10X-RAY DIFFRACTION10AA112 - 117116 - 121
11X-RAY DIFFRACTION11AA118 - 129122 - 133
12X-RAY DIFFRACTION12AA130 - 134134 - 138
13X-RAY DIFFRACTION13AA135 - 141139 - 145
14X-RAY DIFFRACTION14AA142 - 148146 - 152
15X-RAY DIFFRACTION15AA160 - 176164 - 180
16X-RAY DIFFRACTION16AA177 - 190181 - 194
17X-RAY DIFFRACTION17AA191 - 200195 - 204

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