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- PDB-4bk5: crystal structure of the human EphA4 ectodomain in complex with h... -

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Basic information

Entry
Database: PDB / ID: 4bk5
Titlecrystal structure of the human EphA4 ectodomain in complex with human ephrin A5 (amine-methylated sample)
Components
  • EPHRIN TYPE-A RECEPTOR 4
  • EPHRIN-A5Ephrin A5
KeywordsSIGNALING PROTEIN / CELL ADHESION / CELL REPULSION / RECEPTOR CLUSTERING / RECEPTOR CIS INTERACTION / ERYTHROPOETIN-PRODUCING HEPATOCELLULAR RECEPTOR / LBD / EGF / FN
Function / homology
Function and homology information


neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / DH domain binding / neuron projection fasciculation / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / positive regulation of Rho guanyl-nucleotide exchange factor activity / neuron projection guidance / nephric duct morphogenesis ...neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / DH domain binding / neuron projection fasciculation / corticospinal tract morphogenesis / regulation of astrocyte differentiation / negative regulation of proteolysis involved in protein catabolic process / positive regulation of Rho guanyl-nucleotide exchange factor activity / neuron projection guidance / nephric duct morphogenesis / regulation of synapse pruning / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / PH domain binding / glial cell migration / synaptic membrane adhesion / regulation of cell-cell adhesion / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / collateral sprouting / regulation of modification of synaptic structure / cellular response to follicle-stimulating hormone stimulus / positive regulation of collateral sprouting / negative regulation of epithelial to mesenchymal transition / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of dendritic spine morphogenesis / neurotrophin TRKA receptor binding / chemorepellent activity / negative regulation of cell adhesion / adult walking behavior / motor neuron axon guidance / regulation of cell morphogenesis / retinal ganglion cell axon guidance / positive regulation of synapse assembly / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Somitogenesis / regulation of focal adhesion assembly / regulation of axonogenesis / positive regulation of amyloid-beta formation / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of long-term synaptic potentiation / EPH-ephrin mediated repulsion of cells / basement membrane / positive regulation of cell adhesion / GABA-ergic synapse / ephrin receptor signaling pathway / positive regulation of protein tyrosine kinase activity / axon terminus / axonal growth cone / regulation of microtubule cytoskeleton organization / cellular response to forskolin / protein tyrosine kinase binding / ephrin receptor binding / negative regulation of cell migration / dendritic shaft / filopodium / caveola / axon guidance / regulation of actin cytoskeleton organization / postsynaptic density membrane / adherens junction / neuromuscular junction / Schaffer collateral - CA1 synapse / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of neuron projection development / presynaptic membrane / nervous system development / amyloid-beta binding / kinase activity / perikaryon / early endosome membrane / protein tyrosine kinase activity / mitochondrial outer membrane / negative regulation of translation / dendritic spine / protein autophosphorylation / protein stabilization / cell adhesion / protein kinase activity / positive regulation of cell migration / positive regulation of protein phosphorylation / axon / external side of plasma membrane / dendrite / glutamatergic synapse / positive regulation of cell population proliferation
Similarity search - Function
ephrin a2 ectodomain / 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. ...ephrin a2 ectodomain / 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. / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 / Ribbon / 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 / Jelly Rolls / Serine/Threonine protein kinases, catalytic domain / Immunoglobulins / 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-A5 / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Nov 11, 2015Group: Data collection
Revision 1.4Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.5Dec 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

Downloads & links

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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
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-11.2 kcal/mol
Surface area36560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.950, 256.950, 252.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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
Details: SAMPLE WAS AMINE-METHYLATED PRIOR TO CRYSTALLIZATION
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 / 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
Details: SAMPLE WAS AMINE-METHYLATED PRIOR TO CRYSTALLIZATION
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
References: UniProt: P52803, receptor protein-tyrosine kinase
Sequence detailsSEQUENCE CORRESPONDS TO HEPHA4 RESIDUES 27-547 FUSED TO AN N-TERMINAL SECRETION SIGNAL SEQUENCE AND ...SEQUENCE CORRESPONDS TO HEPHA4 RESIDUES 27-547 FUSED TO AN N-TERMINAL SECRETION SIGNAL SEQUENCE AND A POLY-HISTIDINE TAG SEQUENCE CORRESPONDS TO HEPHRINA5 RESIDUES 27-166 FUSED TO AN N-TERMINAL SECRETION SIGNAL SEQUENCE AND A 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 % sol: 88.2 %
Description: WE USED THE NEW CC CRITERIA TO DETERMINE THE HIGH RESOLUTION CUT-OFF. THE CC-HALF VALUE IN THE HIGHEST RES SHELL IS 15.9
Crystal growDetails: 8 % W-V POLYETHYLENE GLYCOL 8000 AND 0.1 M TRIS-HCL PH 8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONDiamond I2411
SYNCHROTRONDiamond I0421
SYNCHROTRONDiamond I04-131
Detector
TypeIDDetector
ADSC CCD1CCD
ADSC CCD2CCD
ADSC CCD3CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→70 Å / Num. obs: 27221 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 130.48 Å2 / Rmerge(I) obs: 0.41 / Net I/σ(I): 7.7
Reflection shellResolution: 4→4.05 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4BK4, 2X11

4bk4

2x11


Resolution: 4→70.41 Å / Cor.coef. Fo:Fc: 0.8006 / Cor.coef. Fo:Fc free: 0.8147 / SU R Cruickshank DPI: 1.078 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1 / SU Rfree Blow DPI: 0.537 / SU Rfree Cruickshank DPI: 0.555
RfactorNum. reflection% reflectionSelection details
Rfree0.3213 1362 5.02 %RANDOM
Rwork0.3125 ---
obs0.313 27150 99.89 %-
Displacement parametersBiso mean: 187.97 Å2
Baniso -1Baniso -2Baniso -3
1--10.6627 Å20 Å20 Å2
2---10.6627 Å20 Å2
3---21.3254 Å2
Refine analyzeLuzzati coordinate error obs: 1.707 Å
Refinement stepCycle: LAST / Resolution: 4→70.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 0 0 5087
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075222HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.877102HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1774SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes755HARMONIC5
X-RAY DIFFRACTIONt_it5222HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.37
X-RAY DIFFRACTIONt_other_torsion21.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion673SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4882SEMIHARMONIC4
LS refinement shellResolution: 4→4.15 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.1972 137 4.86 %
Rwork0.2068 2680 -
all0.2063 2817 -
obs--99.89 %
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)
1-0.3062-0.15310.25891.4491-1.94912.24440.0524-0.10390.01260.274-0.1201-0.0271-0.39060.40290.06770.28730.18090.0556-0.27260.20760.174-33.4676-41.9098-85.9291
23.536-0.50751.0653-0.9773.97575.20730.1175-0.34970.64380.5119-0.1524-0.0266-0.74350.19920.0349-0.26590.1740.0641-0.1158-0.1385-0.2627-4.5671-81.3655-29.8878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN C

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