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- PDB-7s7k: Crystal structure of the EphB2 extracellular domain -

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Basic information

Entry
Database: PDB / ID: 7s7k
TitleCrystal structure of the EphB2 extracellular domain
ComponentsEphrin type-B receptor 2
KeywordsTRANSFERASE / EphB2 / ECD / autoinhibitory
Function / homology
Function and homology information


regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / negative regulation of NMDA glutamate receptor activity / EPH-Ephrin signaling / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity ...regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / negative regulation of NMDA glutamate receptor activity / EPH-Ephrin signaling / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity / regulation of body fluid levels / urogenital system development / postsynaptic membrane assembly / optic nerve morphogenesis / tight junction assembly / neuron projection retraction / axon guidance receptor activity / central nervous system projection neuron axonogenesis / transmembrane-ephrin receptor activity / positive regulation of long-term neuronal synaptic plasticity / negative regulation of axonogenesis / regulation of autophagosome assembly / positive regulation of dendritic spine morphogenesis / dendritic spine development / corpus callosum development / positive regulation of synaptic plasticity / regulation of filopodium assembly / ephrin receptor activity / camera-type eye morphogenesis / regulation of behavioral fear response / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / retinal ganglion cell axon guidance / axonal fasciculation / positive regulation of synapse assembly / regulation of receptor signaling pathway via JAK-STAT / regulation of synapse assembly / inner ear morphogenesis / regulation of axonogenesis / B cell activation / roof of mouth development / regulation of neuronal synaptic plasticity / regulation of blood coagulation / positive regulation of immunoglobulin production / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / positive regulation of B cell proliferation / hippocampal mossy fiber to CA3 synapse / axonogenesis / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / axon guidance / positive regulation of protein localization to plasma membrane / animal organ morphogenesis / negative regulation of protein kinase activity / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of tumor necrosis factor production / presynaptic membrane / signaling receptor activity / amyloid-beta binding / postsynapse / postsynaptic membrane / protein tyrosine kinase activity / angiogenesis / cellular response to lipopolysaccharide / dendritic spine / learning or memory / positive regulation of cell migration / axon / phosphorylation / signaling receptor binding / neuronal cell body / synapse / glutamatergic synapse / dendrite / protein-containing complex binding / positive regulation of gene expression / cell surface / nucleoplasm / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Ephrin type-B receptor 2, 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-B receptor 2, 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 / 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 / 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
Ephrin type-B receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsXu, Y. / Xu, K. / Nikolov, D.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Int J Mol Sci / Year: 2021
Title: The Ephb2 Receptor Uses Homotypic, Head-to-Tail Interactions within Its Ectodomain as an Autoinhibitory Control Mechanism.
Authors: Xu, Y. / Robev, D. / Saha, N. / Wang, B. / Dalva, M.B. / Xu, K. / Himanen, J.P. / Nikolov, D.B.
History
DepositionSep 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,6745
Polymers58,2201
Non-polymers1,4534
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.843, 111.142, 156.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ephrin type-B receptor 2 / Neural kinase / Nuk receptor tyrosine kinase / Tyrosine-protein kinase receptor EPH-3 / Tyrosine- ...Neural kinase / Nuk receptor tyrosine kinase / Tyrosine-protein kinase receptor EPH-3 / Tyrosine-protein kinase receptor SEK-3


Mass: 58220.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ephb2, Epth3, Nuk, Sek3 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P54763, receptor protein-tyrosine kinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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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: 5.53 Å3/Da / Density % sol: 77.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.1 M Na Succinate, 0.1M Na Acetate pH 4.8, 5% (v/v) MPD, and 3% 1, 6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.145→48.4 Å / Num. all: 22540 / Num. obs: 22540 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 116.94 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Rsym value: 0.041 / Net I/av σ(I): 15.3 / Net I/σ(I): 18 / Num. measured all: 73799
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.145-3.323.40.792132930.5441.040.79299.3
3.32-3.523.10.3622.130780.2610.4870.36298
3.52-3.763.40.1824.229350.1260.2430.18299.7
3.76-4.063.40.1027.427410.0740.140.10299.4
4.06-4.453.30.0581324810.0420.0780.05897.8
4.45-4.973.20.03421.422510.0260.0480.03497.3
4.97-5.743.30.02924.720180.0210.0390.02998.2
5.74-7.033.10.02726.616590.0190.0350.02795.2
7.03-9.953.20.01832.413380.0120.0240.01896.8
9.95-48.430.01442.47460.010.0180.01490.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FL7

3fl7


Resolution: 3.15→48.4 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1151 5.12 %
Rwork0.2136 21341 -
obs0.2153 22492 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.92 Å2 / Biso mean: 115.9915 Å2 / Biso min: 52.5 Å2
Refinement stepCycle: final / Resolution: 3.15→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 0 95 0 4167
Biso mean--173.57 --
Num. residues----525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.15-3.290.37551460.34612664281098
3.29-3.460.36081400.29642624276498
3.46-3.680.32321400.28942695283599
3.68-3.960.26471450.24142678282399
3.96-4.360.22411410.20742658279998
4.36-4.990.21521470.17692633278097
4.99-6.280.21571590.19492670282997
6.29-48.40.24521330.19732719285293

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