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- PDB-1kgy: Crystal Structure of the EphB2-ephrinB2 complex -

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Basic information

Entry
Database: PDB / ID: 1kgy
TitleCrystal Structure of the EphB2-ephrinB2 complex
Components
  • EPHRIN TYPE-B RECEPTOR 2
  • EPHRIN-B2
KeywordsTRANSFERASE/TRANSFERASE RECEPTOR / Developmental protein / TRANSFERASE-TRANSFERASE RECEPTOR COMPLEX
Function / homology
Function and homology information


regulation of T-helper 17 type immune response / Ephrin signaling / EPH-Ephrin signaling / hindbrain tangential cell migration / negative regulation of glutamate receptor signaling pathway / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / venous blood vessel morphogenesis / EPHB-mediated forward signaling / nephric duct morphogenesis ...regulation of T-helper 17 type immune response / Ephrin signaling / EPH-Ephrin signaling / hindbrain tangential cell migration / negative regulation of glutamate receptor signaling pathway / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / venous blood vessel morphogenesis / EPHB-mediated forward signaling / nephric duct morphogenesis / optic nerve morphogenesis / urogenital system development / positive regulation of aorta morphogenesis / tight junction assembly / regulation of body fluid levels / neuron projection retraction / central nervous system projection neuron axonogenesis / postsynaptic membrane assembly / positive regulation of cardiac muscle cell differentiation / axon guidance receptor activity / transmembrane-ephrin receptor activity / negative regulation of axonogenesis / presynapse assembly / positive regulation of synaptic plasticity / positive regulation of long-term neuronal synaptic plasticity / corpus callosum development / lymph vessel development / dendritic spine development / camera-type eye morphogenesis / regulation of filopodium assembly / ephrin receptor activity / positive regulation of dendritic spine morphogenesis / regulation of chemotaxis / positive regulation of glutamate receptor signaling pathway / adherens junction organization / regulation of autophagosome assembly / regulation of behavioral fear response / commissural neuron axon guidance / dendritic spine morphogenesis / negative regulation of cell adhesion / negative regulation of Ras protein signal transduction / positive regulation of protein localization to cell surface / axonal fasciculation / phosphorylation / retinal ganglion cell axon guidance / cell migration involved in sprouting angiogenesis / blood vessel morphogenesis / positive regulation of synapse assembly / regulation of receptor signaling pathway via JAK-STAT / inner ear morphogenesis / positive regulation of immunoglobulin production / regulation of axonogenesis / regulation of synapse assembly / regulation of postsynaptic neurotransmitter receptor internalization / regulation of blood coagulation / B cell activation / roof of mouth development / keratinocyte proliferation / regulation of neuronal synaptic plasticity / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / regulation of postsynaptic membrane neurotransmitter receptor levels / ephrin receptor binding / T cell costimulation / positive regulation of B cell proliferation / neuron projection maintenance / negative regulation of cytokine production involved in inflammatory response / axonogenesis / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / hippocampal mossy fiber to CA3 synapse / peptidyl-tyrosine phosphorylation / animal organ morphogenesis / positive regulation of long-term synaptic potentiation / learning / adherens junction / receptor protein-tyrosine kinase / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / Schaffer collateral - CA1 synapse / cell morphogenesis / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / signaling receptor activity / negative regulation of neuron projection development / amyloid-beta binding / presynaptic membrane / cellular response to lipopolysaccharide / protein tyrosine kinase activity / angiogenesis / dendritic spine / postsynaptic membrane / cell differentiation / learning or memory / cell adhesion / positive regulation of cell migration / axon / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation
Similarity search - Function
Ephrin type-B receptor 2, ligand binding domain / Ephrin-B ectodomain / 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 type-B receptor 2, ligand binding domain / Ephrin-B ectodomain / 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 / 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 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsHimanen, J.P. / Rajashankar, K.R. / Lackmann, M. / Cowan, C.A. / Henkemeyer, M. / Nikolov, D.B.
CitationJournal: Nature / Year: 2001
Title: Crystal structure of an Eph receptor-ephrin complex.
Authors: Himanen, J.P. / Rajashankar, K.R. / Lackmann, M. / Cowan, C.A. / Henkemeyer, M. / Nikolov, D.B.
History
DepositionNov 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPHRIN TYPE-B RECEPTOR 2
B: EPHRIN TYPE-B RECEPTOR 2
C: EPHRIN TYPE-B RECEPTOR 2
D: EPHRIN TYPE-B RECEPTOR 2
E: EPHRIN-B2
F: EPHRIN-B2
G: EPHRIN-B2
H: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)146,2908
Polymers146,2908
Non-polymers00
Water00
1
A: EPHRIN TYPE-B RECEPTOR 2
D: EPHRIN TYPE-B RECEPTOR 2
E: EPHRIN-B2
H: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)73,1454
Polymers73,1454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EPHRIN TYPE-B RECEPTOR 2
C: EPHRIN TYPE-B RECEPTOR 2
F: EPHRIN-B2
G: EPHRIN-B2


Theoretical massNumber of molelcules
Total (without water)73,1454
Polymers73,1454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-36 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78, 78, 78
Angle α, β, γ (deg.)69, 75, 69
Int Tables number1
Space group name H-MP1
Detailschains B and F form a heterodimer chains C and D form a heterodimer Chains B, C, F, and G form a proposed heterotetramer

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Components

#1: Protein
EPHRIN TYPE-B RECEPTOR 2


Mass: 20856.512 Da / Num. of mol.: 4 / Fragment: ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P54763, EC: 2.7.1.112
#2: Protein
EPHRIN-B2


Mass: 15715.984 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P52800
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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M Na/K Phosphate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
210 mM1dropKCl
32 mM1dropMgCl2
410 mMHEPES1droppH7.2
51.6 Msodium potassium phospahte1reservoir
6100 mMHEPES-NaOH1reservoirpH7.5

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2000
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 43549 / Num. obs: 42156 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.7→2.82 Å / Rmerge(I) obs: 0.37 / % possible all: 93.5

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→25 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2956 2581 random
Rwork0.2427 --
all-43465 -
obs-42787 -
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10260 0 0 0 10260
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0082
X-RAY DIFFRACTIONx_angle_deg1.6374
Refinement
*PLUS
Rfactor obs: 0.243 / Rfactor Rfree: 0.295
Solvent computation
*PLUS
Displacement parameters
*PLUS

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