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- PDB-2wo3: Crystal Structure of the EphA4-ephrinA2 complex -

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Basic information

Entry
Database: PDB / ID: 2wo3
TitleCrystal Structure of the EphA4-ephrinA2 complex
Components
  • EPHRIN TYPE-A RECEPTOR
  • EPHRIN-A2
KeywordsTRANSFERASE/SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN COMPLEX / EFN / EPH / EPHA4 / KINASE / EPHRIN / COMPLEX / MEMBRANE / CELL SURFACE RECEPTOR / TYROSINE-PROTEIN KINASE / GLYCOPROTEIN / EPHRINA2
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 / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor 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 / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / transmembrane-ephrin receptor activity / glial cell migration / positive regulation of amyloid precursor protein catabolic process / PH domain binding / regulation of modification of synaptic structure / GPI-linked ephrin receptor activity / regulation of synapse pruning / olfactory bulb development / adherens junction organization / positive regulation of dendrite morphogenesis / regulation of dendritic spine morphogenesis / bone remodeling / negative regulation of cell adhesion / motor neuron axon guidance / EPH-Ephrin signaling / innervation / 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 / positive regulation of intracellular signal transduction / negative regulation of long-term synaptic potentiation / cochlea development / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / axonal growth cone / side of membrane / ephrin receptor binding / axon terminus / positive regulation of cell adhesion / axon guidance / protein tyrosine kinase binding / osteoclast differentiation / peptidyl-tyrosine phosphorylation / negative regulation of cell migration / dendritic shaft / positive regulation of JNK cascade / filopodium / adherens junction / 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 / presynaptic membrane / 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 / positive regulation of cell population proliferation / dendrite / glutamatergic synapse / cell surface / ATP binding / identical protein binding / plasma membrane / cytoplasm
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) / 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-A2 / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y.
CitationJournal: Structure / Year: 2009
Title: Structural Plasticity of Eph-Receptor A4 Facilitates Cross-Class Ephrin Signalling
Authors: Bowden, T.A. / Aricescu, A.R. / Nettleship, J.E. / Siebold, C. / Rahman-Huq, N. / Owens, R.J. / Stuart, D.I. / Jones, E.Y.
History
DepositionJul 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED (DSSP).
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED (DSSP).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPHRIN TYPE-A RECEPTOR
B: EPHRIN-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9573
Polymers39,5322
Non-polymers4241
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-2.8 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.412, 115.412, 59.354
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein EPHRIN TYPE-A RECEPTOR / TYROSINE-PROTEIN KINASE RECEPTOR SEK / RECEPTOR PROTEIN-TYROSINE KINASE HEK8 / TYROSINE-PROTEIN KINASE TYRO1


Mass: 21467.191 Da / Num. of mol.: 1 / Fragment: EPHRIN LIGAND BINDING DOMAIN, RESIDUES 30-202
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-A2 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 6 / HEK7-LIGAND / LERK-6 / HEK7-L


Mass: 18065.105 Da / Num. of mol.: 1 / Fragment: EPH RECEPTOR BINDING DOMAIN, RESIDUES 33-177 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE AT ASN 42
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O43921
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, ASN 174 TO GLN
Has protein modificationY
Sequence detailsQ174N SITE-DIRECTED MUTATION TO PROMOTE CRYSTALLOGENESIS

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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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 8 / Details: 20% PEG 3350, 200 MM KNO3, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.81
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 10, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.81 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 18961 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 16 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 30
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KGY

1kgy


Resolution: 2.35→49.97 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.556 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24554 954 5 %RANDOM
Rwork0.19779 ---
obs0.20012 17987 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.59 Å20 Å2
2--1.19 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 28 136 2740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222680
X-RAY DIFFRACTIONr_bond_other_d0.0010.021858
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9573639
X-RAY DIFFRACTIONr_angle_other_deg0.80734463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51323.165139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01715425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3841524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02593
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.751.51582
X-RAY DIFFRACTIONr_mcbond_other0.0991.5640
X-RAY DIFFRACTIONr_mcangle_it1.40922557
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5631098
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6444.51082
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 80 -
Rwork0.442 1295 -
obs--98.78 %
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)
11.8431-0.1820.34980.89360.44484.35410.0767-0.05170.04680.1288-0.2086-0.06730.252-0.25010.13190.0583-0.05320.01520.1686-0.01210.031914.86-44.84827.86
24.4989-0.3875-0.24821.13520.14550.9061-0.0713-0.1605-0.14460.03260.0255-0.0169-0.0320.0740.04580.08860.02150.00530.11420.00190.0082-6.137-40.8949.628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B32 - 173
2X-RAY DIFFRACTION2A28 - 203

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