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- PDB-2x11: Crystal structure of the complete EphA2 ectodomain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2x11
TitleCrystal structure of the complete EphA2 ectodomain in complex with ephrin A5 receptor binding domain
Components
  • EPHRIN TYPE-A RECEPTOR 2
  • EPHRIN-A5
KeywordsRECEPTOR/SIGNALING PROTEIN / RECEPTOR-SIGNALING PROTEIN COMPLEX / DEVELOPMENTAL PROTEIN / SIGNALING PLATFORM / KINASE / TRANSFERASE / NEUROGENESIS / RECEPTOR / CATARACT / APOPTOSIS / ERYTHROPOIETIN-PRODUCING HEPATOCELLULAR CARCINOMA / ANGIOGENESIS / SIGNALING PROTEIN
Function / homology
Function and homology information


neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / negative regulation of substrate adhesion-dependent cell spreading / notochord cell development / notochord formation / synaptic membrane adhesion / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation ...neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / negative regulation of substrate adhesion-dependent cell spreading / notochord cell development / notochord formation / synaptic membrane adhesion / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / collateral sprouting / pericyte cell differentiation / cellular response to follicle-stimulating hormone stimulus / leading edge membrane / regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of collateral sprouting / negative regulation of chemokine production / ephrin receptor activity / activation of GTPase activity / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase activator activity / post-anal tail morphogenesis / response to growth factor / chemorepellent activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of bicellular tight junction assembly / bone remodeling / regulation of lamellipodium assembly / regulation of GTPase activity / negative regulation of cell adhesion mediated by integrin / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / regulation of cell morphogenesis / retinal ganglion cell axon guidance / positive regulation of synapse assembly / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / tight junction / regulation of focal adhesion assembly / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell-cell adhesion / RHOU GTPase cycle / lamellipodium membrane / basement membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / vasculogenesis / regulation of ERK1 and ERK2 cascade / keratinocyte differentiation / ephrin receptor binding / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / osteoclast differentiation / cellular response to forskolin / cell surface receptor protein tyrosine kinase signaling pathway / molecular function activator activity / negative regulation of angiogenesis / axon guidance / regulation of microtubule cytoskeleton organization / protein localization to plasma membrane / regulation of actin cytoskeleton organization / cell chemotaxis / positive regulation of protein localization to plasma membrane / skeletal system development / adherens junction / cell motility / receptor protein-tyrosine kinase / caveola / GABA-ergic synapse / intrinsic apoptotic signaling pathway in response to DNA damage / ruffle membrane / osteoblast differentiation / nervous system development / cell migration / lamellipodium / virus receptor activity / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / signaling receptor complex / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / receptor ligand activity / external side of plasma membrane / focal adhesion / cell surface
Similarity search - Function
Ephrin-A ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Ephrin type-A receptor 2, ligand binding domain / Ephrin cysteine rich domain / Ephrin receptor type-A /type-B ...Ephrin-A ectodomain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Ephrin type-A receptor 2, ligand binding domain / Ephrin cysteine rich domain / 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 / Growth factor receptor cysteine-rich domain superfamily / 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 / 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 type-A receptor 2 / Ephrin-A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.83 Å
AuthorsSeiradake, E. / Harlos, K. / Sutton, G. / Aricescu, A.R. / Jones, E.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: An Extracellular Steric Seeding Mechanism for Eph-Ephrin Signalling Platform Assembly
Authors: Seiradake, E. / Harlos, K. / Sutton, G. / Aricescu, A.R. / Jones, E.Y.
History
DepositionDec 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2Feb 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_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPHRIN TYPE-A RECEPTOR 2
B: EPHRIN-A5


Theoretical massNumber of molelcules
Total (without water)80,2622
Polymers80,2622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-11.6 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.630, 59.630, 112.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein EPHRIN TYPE-A RECEPTOR 2 / TYROSINE-PROTEIN KINASE RECEPTOR ECK / EPITHELIAL CELL KINASE / EPHA2


Mass: 59859.215 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 27-534
Source method: isolated from a genetically manipulated source
Details: NAG ON ASN407, DI-METHYLATION OF LYSINES / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): GNTI-DEFICIENT
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein EPHRIN-A5 / EPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 7 / LERK-7 / AL-1 / HUMAN EPHRIN A5


Mass: 20402.324 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 26-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): GNTI-DEFICIENT / References: UniProt: P52803
Has protein modificationY
Sequence detailsCONTAINS FOREIGN SIGNAL PEPTIDE AND POLY-HIS TAG

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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: 3.61 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growDetails: TWO PARTS OF PROTEIN SOLUTION WERE MIXED WITH ONE PART WATER, ONE PART RESERVOIR SOLUTION (8 % POLYETHYLENE GLYCOL 6000, 0.8 M LICL, 0.08 M CITRATE PH 5) AND ONE PART 1 % POLYVINYLPYRROLIDONE K15.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 4.8→173 Å / Num. obs: 6016 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 166.11 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.95
Reflection shellResolution: 4.8→4.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.8 / % possible all: 75.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3CZU, 3FL7, 1SHW

3czu

3fl7

1shw


Resolution: 4.83→40.482 Å / σ(F): 0.03 / Phase error: 34 / Stereochemistry target values: ML
Details: DUE TO LOW RESOLUTION, THE REFINEMENT PROTOCOL WAS LIMITED TO THE FOLLOWING THREE STEPS AFTER MOLECULAR REPLACEMENT. 1. RIGID BODY REFINEMENT OF INDIVIDUAL DOMAINS 2. TLS REFINEMENT OF ...Details: DUE TO LOW RESOLUTION, THE REFINEMENT PROTOCOL WAS LIMITED TO THE FOLLOWING THREE STEPS AFTER MOLECULAR REPLACEMENT. 1. RIGID BODY REFINEMENT OF INDIVIDUAL DOMAINS 2. TLS REFINEMENT OF SELECTED PORTIONS 3. STRUCTURE REGULARIZATION TO AVOID MINOR CLASHES. WE PERFORMED NO INDIVIDUAL ATOM REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.3143 260 4.6 %
Rwork0.3123 --
obs0.313 5643 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--46.5561 Å2-0 Å20 Å2
2---4.8023 Å20 Å2
3---48.1254 Å2
Refinement stepCycle: LAST / Resolution: 4.83→40.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 0 0 4870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035039
X-RAY DIFFRACTIONf_angle_d0.6756844
X-RAY DIFFRACTIONf_dihedral_angle_d17.7071778
X-RAY DIFFRACTIONf_chiral_restr0.044729
X-RAY DIFFRACTIONf_plane_restr0.004901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.8261-6.07710.33411170.34012537X-RAY DIFFRACTION90
6.0771-40.4830.30741430.30122846X-RAY DIFFRACTION97

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