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- PDB-2hle: Structural and biophysical characterization of the EPHB4-EPHRINB2... -

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Basic information

Entry
Database: PDB / ID: 2hle
TitleStructural and biophysical characterization of the EPHB4-EPHRINB2 protein protein interaction and receptor specificity.
Components
  • Ephrin type-B receptor 4
  • Ephrin-B2
KeywordsTRANSFERASE/TRANSFERASE RECEPTOR / Protein-protein interaction / Receptor tryosine kinase / Bi-directional cell signaling / TRANSFERASE-TRANSFERASE RECEPTOR COMPLEX / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D
Function / homology
Function and homology information


venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / ephrin receptor activity / positive regulation of cardiac muscle cell differentiation / presynapse assembly / lymph vessel development / regulation of chemotaxis / adherens junction organization / cell migration involved in sprouting angiogenesis ...venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / ephrin receptor activity / positive regulation of cardiac muscle cell differentiation / presynapse assembly / lymph vessel development / regulation of chemotaxis / adherens junction organization / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / blood vessel morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / anatomical structure morphogenesis / negative regulation of keratinocyte proliferation / regulation of postsynaptic membrane neurotransmitter receptor levels / heart morphogenesis / ephrin receptor binding / T cell costimulation / transmembrane receptor protein tyrosine kinase activity / EPHB-mediated forward signaling / axon guidance / animal organ morphogenesis / adherens junction / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / postsynaptic density membrane / 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 / Schaffer collateral - CA1 synapse / cell-cell signaling / presynaptic membrane / negative regulation of neuron projection development / virus receptor activity / cellular response to lipopolysaccharide / protein autophosphorylation / angiogenesis / receptor complex / cell adhesion / focal adhesion / positive regulation of cell population proliferation / dendrite / glutamatergic synapse / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin-B ectodomain / Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Tyrosine-protein kinase ephrin type A/B receptor-like ...Ephrin-B ectodomain / Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / 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) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Cupredoxins - blue copper proteins / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / EGF-like domain signature 2. / Cupredoxin / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin-B2 / Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChrencik, J.E. / Brooun, A. / Kuhn, P. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Biophysical Characterization of the EphB4-EphrinB2 Protein-Protein Interaction and Receptor Specificity.
Authors: Chrencik, J.E. / Brooun, A. / Kraus, M.L. / Recht, M.I. / Kolatkar, A.R. / Han, G.W. / Seifert, J.M. / Widmer, H. / Auer, M. / Kuhn, P.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-B receptor 4
B: Ephrin-B2


Theoretical massNumber of molelcules
Total (without water)37,1412
Polymers37,1412
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-9 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.085, 81.085, 50.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Ephrin type-B receptor 4 / Tyrosine-protein kinase receptor HTK / EPHB4


Mass: 21354.230 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Hi5 / Gene: EPHB4, HTK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P54760, receptor protein-tyrosine kinase
#2: Protein Ephrin-B2 / EPH-related receptor tyrosine kinase ligand 5 / LERK-5 / HTK ligand / HTK-L / EPHRINB2


Mass: 15787.061 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Hi5 / Gene: EFNB2, EPLG5, HTKL, LERK5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P52799
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 2.2 M Ammonium sulfate, 100 mM Tris, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 19785 / % possible obs: 99.63 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.05→2.103 Å / % possible all: 99.93

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KGY

1kgy


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.808 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.245 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 74, 96-99 IN B MOLECULE WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29521 1064 5.1 %RANDOM
Rwork0.22567 ---
obs0.22928 19785 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 79 2546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222555
X-RAY DIFFRACTIONr_bond_other_d0.0030.021660
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9463490
X-RAY DIFFRACTIONr_angle_other_deg1.0183.0044053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7485324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.95124.324111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.49515393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.097159
X-RAY DIFFRACTIONr_chiral_restr0.1050.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
X-RAY DIFFRACTIONr_nbd_refined0.210.2427
X-RAY DIFFRACTIONr_nbd_other0.2080.21656
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21119
X-RAY DIFFRACTIONr_nbtor_other0.0920.21420
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1280.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.40731678
X-RAY DIFFRACTIONr_mcbond_other0.6423652
X-RAY DIFFRACTIONr_mcangle_it3.43152577
X-RAY DIFFRACTIONr_scbond_it5.86481056
X-RAY DIFFRACTIONr_scangle_it7.1411910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 79 -
Rwork0.265 1435 -
obs--99.93 %
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)
12.3431.4979-1.35773.1049-1.18622.4417-0.05980.14780.09160.6662-0.0475-0.1015-0.37160.06120.1072-0.33730.0382-0.0356-0.3270.1583-0.01828.806635.8129-6.1113
25.5617-1.8386-0.51493.53670.54411.5216-0.16540.4142-0.05220.22660.13030.4063-0.120.19760.0351-0.32020.00590.0101-0.25250.078-0.22988.373226.0832-6.9463
33.4177-0.43140.15735.56041.08490.5746-0.08691.08520.3042-0.44570.04690.4696-0.11780.14880.04-0.26890.0081-0.1076-0.16160.1954-0.17654.385429.2097-11.3244
41.84680.54741.70043.66091.30855.34380.3796-0.4033-0.46810.6758-0.0002-0.06090.69650.1758-0.37940.30040.0679-0.0191-0.09940.1231-0.200518.4522.704318.2199
58.30862.54992.09447.73040.63187.8664-0.28240.67260.18210.52080.36090.1375-0.50471.2714-0.0786-0.17440.0158-0.0853-0.00560.1244-0.310326.469631.788412.9329
61.80761.15622.88211.71611.60685.45820.44190.262-0.56330.56470.1543-0.41880.81650.922-0.59610.02170.1585-0.10490.03040.011-0.101624.563422.04269.6675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 421 - 34
2X-RAY DIFFRACTION2AA43 - 10635 - 98
3X-RAY DIFFRACTION3AA107 - 19699 - 188
4X-RAY DIFFRACTION4BB31 - 641 - 34
5X-RAY DIFFRACTION5BB65 - 10935 - 79
6X-RAY DIFFRACTION6BB110 - 16880 - 138

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