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- PDB-3gxu: Crystal structure of Eph receptor and ephrin complex -

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Basic information

Entry
Database: PDB / ID: 3gxu
TitleCrystal structure of Eph receptor and ephrin complex
Components
  • Ephrin type-A receptor 4
  • Ephrin-B2
KeywordsTRANSFERASE / Complex structure / Eph / ephrin / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase / Developmental protein / Differentiation / Disulfide bond / Host-virus interaction / Neurogenesis
Function / homology
Function and homology information


DH domain binding / neuron projection fasciculation / : / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / regulation of astrocyte differentiation / neuron projection guidance / venous blood vessel morphogenesis / nephric duct morphogenesis / fasciculation of sensory neuron axon ...DH domain binding / neuron projection fasciculation / : / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / regulation of astrocyte differentiation / neuron projection guidance / venous blood vessel morphogenesis / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / positive regulation of aorta morphogenesis / synapse pruning / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / positive regulation of cardiac muscle cell differentiation / transmembrane-ephrin receptor activity / glial cell migration / positive regulation of amyloid precursor protein catabolic process / presynapse assembly / PH domain binding / regulation of modification of synaptic structure / GPI-linked ephrin receptor activity / regulation of synapse pruning / lymph vessel development / regulation of chemotaxis / adherens junction organization / positive regulation of dendrite morphogenesis / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / blood vessel morphogenesis / innervation / Ephrin signaling / adult walking behavior / regulation of GTPase activity / negative regulation of epithelial to mesenchymal transition / Somitogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of intracellular signal transduction / negative regulation of long-term synaptic potentiation / cochlea development / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / negative regulation of keratinocyte proliferation / ephrin receptor signaling pathway / axonal growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / ephrin receptor binding / T cell costimulation / axon terminus / EPHB-mediated forward signaling / positive regulation of cell adhesion / axon guidance / protein tyrosine kinase binding / peptidyl-tyrosine phosphorylation / negative regulation of cell migration / animal organ morphogenesis / dendritic shaft / positive regulation of JNK cascade / adherens junction / filopodium / neuromuscular junction / receptor protein-tyrosine kinase / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / kinase activity / cell-cell signaling / negative regulation of neuron projection development / amyloid-beta binding / protein autophosphorylation / cellular response to lipopolysaccharide / presynaptic membrane / virus receptor activity / protein tyrosine kinase activity / early endosome membrane / perikaryon / dendritic spine / negative regulation of neuron apoptotic process / mitochondrial outer membrane / protein kinase activity / cell adhesion / negative regulation of translation / protein stabilization / positive regulation of cell migration / axon / focal adhesion / positive regulation of cell population proliferation / dendrite / glutamatergic synapse / cell surface / ATP binding
Similarity search - Function
Ephrin-B ectodomain / Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding 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-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding 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 / 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 / Serine/Threonine protein kinases, 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin-B2 / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsQin, H.N. / Song, J.X.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Structural characterization of the EphA4-ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity
Authors: Qin, H. / Noberini, R. / Huan, X. / Shi, J. / Pasquale, E.B. / Song, J.
#1: Journal: J.Biol.Chem. / Year: 2008
Title: Crystal structure and NMR binding reveal that two small molecule antagonists target the high affinity ephrin-binding channel of the EphA4 receptor
Authors: Qin, H. / Shi, J. / Noberini, R. / Pasquale, E.B. / Song, J.
#2: Journal: 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
DepositionApr 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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-A receptor 4
B: Ephrin-B2


Theoretical massNumber of molelcules
Total (without water)36,4682
Polymers36,4682
Non-polymers00
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-12 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.651, 48.711, 64.469
Angle α, β, γ (deg.)90.00, 110.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin type-A receptor 4 / Tyrosine-protein kinase receptor SEK / Receptor protein-tyrosine kinase HEK8 / Tyrosine-protein kinase TYRO1


Mass: 20206.844 Da / Num. of mol.: 1 / Fragment: UNP residues 29-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA4, HEK8, SEK, TYRO1 / Plasmid: PET32a / Production host: Escherichia coli (E. coli)
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Protein Ephrin-B2 / EPH-related receptor tyrosine kinase ligand 5 / LERK-5 / HTK ligand / HTK-L


Mass: 16261.525 Da / Num. of mol.: 1 / Fragment: UNP residues 27-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFNB2, EPLG5, HTKL, LERK5 / Plasmid: PET32a / Production host: Escherichia coli (E. coli) / References: UniProt: P52799
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23.5% PEG4000, 0.1M Tris, 0.2M MgCl2, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 11071 / Num. obs: 10938

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CKH, 1KGY

3ckh

1kgy


Resolution: 2.5→25 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.273 405 -
Rwork0.182 --
all0.33 11189 -
obs0.273 10225 98.8 %
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 0 337 2831

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