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- PDB-4m4p: Crystal structure of EPHA4 ectodomain -

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Basic information

Entry
Database: PDB / ID: 4m4p
TitleCrystal structure of EPHA4 ectodomain
ComponentsEphrin type-A receptor 4
KeywordsTRANSFERASE / eph receptor protein kinase
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 / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / glial cell migration / PH domain binding / GPI-linked ephrin receptor activity / regulation of modification of synaptic structure / transmembrane-ephrin receptor activity / regulation of dendritic spine morphogenesis / negative regulation of epithelial to mesenchymal transition / negative regulation of cell adhesion / motor neuron axon guidance / adult walking behavior / adherens junction organization / positive regulation of dendrite morphogenesis / EPH-Ephrin signaling / Somitogenesis / positive regulation of amyloid-beta formation / regulation of axonogenesis / cochlea development / regulation of GTPase activity / EPHA-mediated growth cone collapse / positive regulation of cell adhesion / positive regulation of protein tyrosine kinase activity / negative regulation of long-term synaptic potentiation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / axon terminus / axonal growth cone / ephrin receptor binding / negative regulation of cell migration / protein tyrosine kinase binding / 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 / kinase activity / amyloid-beta binding / early endosome membrane / perikaryon / 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: 2.081 Å
AuthorsXu, K. / Tsvetkova-Robev, D. / Xu, Y. / Goldgur, Y. / Chan, Y.-P. / Himanen, J.P. / Nikolov, D.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Insights into Eph receptor tyrosine kinase activation from crystal structures of the EphA4 ectodomain and its complex with ephrin-A5.
Authors: Xu, K. / Tzvetkova-Robev, D. / Xu, Y. / Goldgur, Y. / Chan, Y.P. / Himanen, J.P. / Nikolov, D.B.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2814
Polymers57,4141
Non-polymers8673
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.589, 112.589, 49.552
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: 57414.156 Da / Num. of mol.: 1 / Fragment: UNP residues 27-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA4, HEK8, SEK, TYRO1 / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): high5
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 22% PEG400, 0.1M MES buffer pH 6.0, 3% DMSO, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→27 Å / Num. all: 42116 / Num. obs: 42061 / % possible obs: 99.87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fl7

3fl7


Resolution: 2.081→27 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.6 / Stereochemistry target values: ML
Details: THE AUTHORS STATE THAT THE CONFORMATION ISSUE FOR NAG601A AS WELL AS THE HIGH REAL SPACE R-FACTORS FOR NAG601A AND NAG602A ARE DUE TO THE PARTIAL DISORDER. THE DENSITY IS OF POOR QUALITY AND ...Details: THE AUTHORS STATE THAT THE CONFORMATION ISSUE FOR NAG601A AS WELL AS THE HIGH REAL SPACE R-FACTORS FOR NAG601A AND NAG602A ARE DUE TO THE PARTIAL DISORDER. THE DENSITY IS OF POOR QUALITY AND THE MODEL PRIMARILY REFLECTS THAT THEY ARE THERE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1978 4.7 %random
Rwork0.1887 ---
obs0.1904 42061 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.081→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 56 161 4214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094155
X-RAY DIFFRACTIONf_angle_d1.3555641
X-RAY DIFFRACTIONf_dihedral_angle_d16.8881541
X-RAY DIFFRACTIONf_chiral_restr0.111635
X-RAY DIFFRACTIONf_plane_restr0.007732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0806-2.13260.27711340.24452826X-RAY DIFFRACTION100
2.1326-2.19020.24141420.23062884X-RAY DIFFRACTION100
2.1902-2.25460.27561380.22962870X-RAY DIFFRACTION100
2.2546-2.32740.28991480.21472872X-RAY DIFFRACTION100
2.3274-2.41050.24561520.21272835X-RAY DIFFRACTION100
2.4105-2.5070.24731420.2022893X-RAY DIFFRACTION100
2.507-2.6210.2981360.21052898X-RAY DIFFRACTION100
2.621-2.7590.26681420.2012816X-RAY DIFFRACTION100
2.759-2.93170.2421400.20412895X-RAY DIFFRACTION100
2.9317-3.15770.20871380.19842855X-RAY DIFFRACTION100
3.1577-3.47490.24621330.19892873X-RAY DIFFRACTION100
3.4749-3.97640.23971430.17642891X-RAY DIFFRACTION100
3.9764-5.00480.17561510.15562836X-RAY DIFFRACTION100
5.0048-27.17950.1911390.17732839X-RAY DIFFRACTION99
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)
11.9448-1.9503-1.09972.48521.52291.13420.2234-0.14671.0018-0.65480.0231-1.1005-0.78160.31090.12230.3597-0.03760.08210.33580.11790.4758-33.133339.1031-4.0756
22.4881-1.4618-0.23273.47610.26631.5378-0.0764-0.00170.17250.15030.0175-0.2528-0.04060.1550.03670.2739-0.0066-0.02660.31270.0580.2693-38.127431.60063.3743
32.0811-0.27250.51710.74090.2611.1206-0.08490.06970.2769-0.12540.2177-0.58610.01580.83880.14790.28460.08330.05190.8937-0.00070.74521.077310.2088-4.2614
40.93770.0435-0.43520.3039-0.3980.93360.31531.3824-0.7429-0.17330.00520.3780.6575-0.85630.53150.49650.0159-0.09491.1874-0.66521.353152.8931-8.1458-5.3091
52.50540.17330.03342.57031.7793.3513-0.01570.0169-0.62630.1680.0528-0.20180.36450.1523-0.02220.34290.0570.01760.402-0.00050.430570.91597.530515.8514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 202 )
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 305 )
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 446 )
5X-RAY DIFFRACTION5chain 'A' and (resid 447 through 542 )

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