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- PDB-4bka: crystal structure of the human EphA4 ectodomain in complex with h... -

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Basic information

Entry
Database: PDB / ID: 4bka
Titlecrystal structure of the human EphA4 ectodomain in complex with human ephrin A5
Components
  • EPHRIN TYPE-A RECEPTOR 4
  • EPHRIN-A5
KeywordsCELL ADHESION / CELL REPULSION / RECEPTOR CLUSTERING / RECEPTOR CIS INTERACTION / EPH-EPHRIN / EPH ECTODOMAIN / ERYTHROPOETIN-PRODUCING HEPATOCELLULAR RECEPTOR / LBD / SUSHI / EGF / FN
Function / homology
Function and homology information


neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / DH domain binding / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / neuron projection guidance / nephric duct morphogenesis ...neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / DH domain binding / neuron projection fasciculation / positive regulation of Rho guanyl-nucleotide exchange factor activity / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / neuron projection guidance / nephric duct morphogenesis / regulation of synapse pruning / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cellular response to hypoxia / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of axon regeneration / glial cell migration / regulation of cell-cell adhesion / synaptic membrane adhesion / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / cellular response to follicle-stimulating hormone stimulus / collateral sprouting / positive regulation of collateral sprouting / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of dendritic spine morphogenesis / chemorepellent activity / neurotrophin TRKA receptor binding / transmembrane-ephrin receptor activity / negative regulation of cell adhesion / negative regulation of epithelial to mesenchymal transition / regulation of cell morphogenesis / adult walking behavior / motor neuron axon guidance / positive regulation of synapse assembly / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Somitogenesis / regulation of focal adhesion assembly / retinal ganglion cell axon guidance / positive regulation of amyloid-beta formation / regulation of axonogenesis / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of protein tyrosine kinase activity / positive regulation of cell adhesion / negative regulation of long-term synaptic potentiation / basement membrane / EPH-ephrin mediated repulsion of cells / GABA-ergic synapse / ephrin receptor signaling pathway / axonal growth cone / regulation of microtubule cytoskeleton organization / axon terminus / cellular response to forskolin / ephrin receptor binding / negative regulation of cell migration / protein tyrosine kinase binding / dendritic shaft / filopodium / caveola / regulation of actin cytoskeleton organization / adherens junction / postsynaptic density membrane / axon guidance / Schaffer collateral - CA1 synapse / neuromuscular junction / receptor protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of neuron projection development / presynaptic membrane / kinase activity / nervous system development / amyloid-beta binding / early endosome membrane / perikaryon / protein tyrosine kinase activity / mitochondrial outer membrane / protein autophosphorylation / dendritic spine / protein stabilization / negative regulation of translation / cell adhesion / protein kinase activity / positive regulation of cell migration / positive regulation of protein phosphorylation / axon / external side of plasma membrane / glutamatergic synapse / dendrite / positive regulation of cell population proliferation
Similarity search - Function
Ephrin-A 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-A 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) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
Similarity search - Domain/homology
Ephrin-A5 / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.3 Å
AuthorsSeiradake, E. / Schaupp, A. / del Toro Ruiz, D. / Kaufmann, R. / Mitakidis, N. / Harlos, K. / Aricescu, A.R. / Klein, R. / Jones, E.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structurally Encoded Intraclass Differences in Epha Clusters Drive Distinct Cell Responses
Authors: Seiradake, E. / Schaupp, A. / Del Toro Ruiz, D. / Kaufmann, R. / Mitakidis, N. / Harlos, K. / Aricescu, A.R. / Klein, R. / Jones, E.Y.
History
DepositionApr 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Oct 21, 2015Group: Data collection
Revision 1.4Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_radiation
Item: _diffrn.ambient_temp / _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.5Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPHRIN TYPE-A RECEPTOR 4
C: EPHRIN-A5


Theoretical massNumber of molelcules
Total (without water)83,3392
Polymers83,3392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)202.628, 202.628, 326.225
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-422-

TYR

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Components

#1: Protein EPHRIN TYPE-A RECEPTOR 4 / EPH-LIKE KINASE 8 / EK8 / HEK8 / TYROSINE-PROTEIN KINASE TYRO1 / TYROSINE-PROTEIN KINASE RECEPTOR SEK


Mass: 62649.336 Da / Num. of mol.: 1 / Fragment: HEPHA4 ECTODOMAIN, RESIDUES 20-547
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Protein EPHRIN-A5 / AL-1 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 7 / LERK-7


Mass: 20689.596 Da / Num. of mol.: 1
Fragment: HEPHRINA5 RECEPTOR BINDING DOMAIN, RESIDUES 27-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P52803
Sequence detailsCONTAINS ARTIFICIAL N-TERMINAL SECRETION SIGNAL AND C- TERMINAL POLY-HISTIDINE TAG CONTAINS ...CONTAINS ARTIFICIAL N-TERMINAL SECRETION SIGNAL AND C- TERMINAL POLY-HISTIDINE TAG CONTAINS ARTIFICIAL N-TERMINAL SECRETION SIGNAL AND C- TERMINAL POLY-HISTIDINE TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 9.05 Å3/Da / Density % sol: 85.3 % / Description: NONE
Crystal growDetails: 0.01 M MGSO4, 1.8 M LISO4, 0.05 M SODIUM CACODYLATE PH 6 AND ADDITIVE 4% BENZAMIDINE-HCL

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONDiamond I2410.9786
SYNCHROTRONDiamond I0420.9786
SYNCHROTRONDiamond I04-130.916
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.9161
ReflectionResolution: 4.95→48 Å / Num. obs: 11758 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.74 / Net I/σ(I): 3.32
Reflection shellResolution: 4.95→5 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 0.32 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BK5

4bk5


Resolution: 5.3→84.87 Å / Cor.coef. Fo:Fc: 0.727 / Cor.coef. Fo:Fc free: 0.684 / SU B: 0.008 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 1.588 / ESU R Free: 1.688 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY RIGID BODY AND TLS REFINEMENT WERE PERFORMED, NO INDIVIDUAL ATOM POSITIONS WERE REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.40753 447 4.8 %RANDOM
Rwork0.38317 ---
obs0.38431 8821 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 243.358 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å23.05 Å20 Å2
2--3.05 Å20 Å2
3----9.89 Å2
Refinement stepCycle: LAST / Resolution: 5.3→84.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 0 0 5087
LS refinement shellResolution: 5.3→5.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 39 -
Rwork0.4 633 -
obs--97.39 %

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