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- PDB-4bk4: crystal structure of the human EphA4 ectodomain -

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Basic information

Entry
Database: PDB / ID: 4bk4
Titlecrystal structure of the human EphA4 ectodomain
ComponentsEPHRIN TYPE-A RECEPTOR 4
KeywordsSIGNALING PROTEIN / CELL ADHESION / CELL REPULSION / RECEPTOR CLUSTERING / RECEPTOR CIS INTERACTION / EPH-EPHRIN CRYSTAL STRUCTURES / EPH ECTODOMAIN / ERYTHROPOETIN-PRODUCING HEPATOCELLULAR RECEPTOR / LBD / EGF / FN
Function / homology
Function and homology information


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 ...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 / 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 / glial cell migration / transmembrane-ephrin receptor activity / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / negative regulation of epithelial to mesenchymal transition / regulation of dendritic spine morphogenesis / negative regulation of cell adhesion / motor neuron axon guidance / adult walking behavior / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Somitogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / negative regulation of long-term synaptic potentiation / positive regulation of cell adhesion / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / positive regulation of protein tyrosine kinase activity / axon terminus / axonal growth cone / protein tyrosine kinase binding / ephrin receptor binding / negative regulation of cell migration / dendritic shaft / filopodium / axon guidance / postsynaptic density membrane / adherens junction / Schaffer collateral - CA1 synapse / neuromuscular junction / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / negative regulation of neuron projection development / presynaptic membrane / amyloid-beta binding / kinase activity / perikaryon / early endosome membrane / protein tyrosine kinase activity / mitochondrial outer membrane / dendritic spine / protein autophosphorylation / negative regulation of translation / protein stabilization / cell adhesion / protein kinase activity / positive regulation of cell migration / axon / glutamatergic synapse / dendrite / positive regulation of cell population proliferation / cell surface / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
ephrin a2 ectodomain / Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / 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 a2 ectodomain / Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / 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 / Sterile alpha motif/pointed 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 / 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 type-A receptor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 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
B: EPHRIN TYPE-A RECEPTOR 4


Theoretical massNumber of molelcules
Total (without water)125,2992
Polymers125,2992
Non-polymers00
Water0
1
A: EPHRIN TYPE-A RECEPTOR 4


Theoretical massNumber of molelcules
Total (without water)62,6491
Polymers62,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPHRIN TYPE-A RECEPTOR 4


Theoretical massNumber of molelcules
Total (without water)62,6491
Polymers62,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)166.890, 166.890, 192.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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.: 2 / 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
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.16 Å3/Da / Density % sol: 76.7 %
Description: WE USED THE NEW CC CUTOFF CRITERIA FOR DETERMINING THE HIGH RES CUTOFF. CC-HALF IN THE HIGH RES SHELL IS 17.7
Crystal growDetails: 1.8 M AMMONIUM PHOSPHATE, 100 MM HEPES PH 7.4, ADDITIVE = EPHRINB2 IN A 1:1 MOLAR RATIO. WE SAW NO SIGN OF EPHRINB2 IN THE CRYSTAL STRUCTURE. THE USUAL BINDING SITE ON HEPHA4 WAS OCCUPIED BY ...Details: 1.8 M AMMONIUM PHOSPHATE, 100 MM HEPES PH 7.4, ADDITIVE = EPHRINB2 IN A 1:1 MOLAR RATIO. WE SAW NO SIGN OF EPHRINB2 IN THE CRYSTAL STRUCTURE. THE USUAL BINDING SITE ON HEPHA4 WAS OCCUPIED BY AN EPHA4-EPHA4 CRYSTAL CONTACT.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONDiamond I2410.9173
SYNCHROTRONDiamond I0420.9173
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 3.65→83 Å / Num. obs: 34863 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 20 % / Biso Wilson estimate: 144.4 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 14.7
Reflection shellResolution: 3.65→3.7 Å / Redundancy: 20 % / Mean I/σ(I) obs: 0.48 / % 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 ENTRY 2X10

2x10


Resolution: 3.65→48.18 Å / Cor.coef. Fo:Fc: 0.7358 / Cor.coef. Fo:Fc free: 0.6986 / SU R Cruickshank DPI: 1.041 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.995 / SU Rfree Blow DPI: 0.584 / SU Rfree Cruickshank DPI: 0.599
RfactorNum. reflection% reflectionSelection details
Rfree0.3858 1753 5.03 %RANDOM
Rwork0.3495 ---
obs0.3513 34842 99.91 %-
Displacement parametersBiso mean: 124.97 Å2
Baniso -1Baniso -2Baniso -3
1--7.8639 Å20 Å20 Å2
2---7.8639 Å20 Å2
3---15.7278 Å2
Refine analyzeLuzzati coordinate error obs: 1.667 Å
Refinement stepCycle: LAST / Resolution: 3.65→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 0 0 6344
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076496HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.858839HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2230SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes180HARMONIC2
X-RAY DIFFRACTIONt_gen_planes936HARMONIC5
X-RAY DIFFRACTIONt_it6496HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.21
X-RAY DIFFRACTIONt_other_torsion21.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion861SEMIHARMONIC5
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_contact6305SEMIHARMONIC4
LS refinement shellResolution: 3.65→3.76 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2201 133 4.51 %
Rwork0.2057 2818 -
all0.2064 2951 -
obs--99.91 %
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)
10.4879-0.3543-0.44930.05340.21510.20470.1445-0.08910.03740.0842-0.05940.0671-0.02620.0635-0.08510.58660.10240.06660.54780.03490.534-25.934659.929341.8729
2-0.25350.99190.18231.35280.21840.1742-0.0727-0.09890.32210.0802-0.0440.1660.22960.01350.11670.54170.0802-0.2070.5672-0.15390.6483-8.83711.2763-6.345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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