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- PDB-2x10: Crystal structure of the complete EphA2 ectodomain -

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Basic information

Entry
Database: PDB / ID: 2x10
TitleCrystal structure of the complete EphA2 ectodomain
ComponentsEPHRIN TYPE-A RECEPTOR 2
KeywordsRECEPTOR / TRANSFERASE / ANGIOGENESIS / KINASE / CATARACT / APOPTOSIS / GLYCOPROTEIN
Function / homology
Function and homology information


notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / response to growth factor / activation of GTPase activity / tight junction / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / regulation of ERK1 and ERK2 cascade / negative regulation of angiogenesis / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / cadherin binding / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
ephrin a2 ectodomain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Ephrin type-A receptor 2, ligand binding 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 a2 ectodomain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Ephrin type-A receptor 2, ligand binding 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) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.1Jan 30, 2013Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / 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 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6793
Polymers60,4221
Non-polymers2572
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.920, 44.650, 93.420
Angle α, β, γ (deg.)93.02, 98.22, 112.12
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 60421.949 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
Nonpolymer detailsN-ACETYLGLUCOSAMINE: ON ASN 407
Sequence detailsINCLUDES FOREIGN N-TERMINAL SIGNAL PEPTIDE AND C-TERMINAL POLY-HIS TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.21 %
Description: USED PHASES FROM MOLECULAR REPLACEMENT DURING SEARCH FOR SE SITES IN PHASER
Crystal growDetails: 1/3 V/V: PROTEIN, 1/3 V/V: 20 % POLYETHYLENE GLYCOL 6000, 1 M LICL, 0.1 M TRIS PH 8 1/3 V/V: 0.4 M NON-DETERGENT SULFOBETAINE 256

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→91 Å / Num. obs: 23406 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 1.71 % / Biso Wilson estimate: 53.68 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.1 Å / Redundancy: 1.22 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.6 / % possible all: 82.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3C8X, 2E7H, 1X5L

3c8x

2e7h

1x5l


Resolution: 3→45.917 Å / SU ML: 1.11 / σ(F): 1.98 / Phase error: 33.6 / Stereochemistry target values: ML
Details: THE DATA INCLUDES UP TO 2.75 A RESOLUTION, FRIEDEL PAIRS UNMERGED. MERGED PAIRS, UP TO 3A RESOLUTION WERE USED FOR REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2986 594 4.9 %
Rwork0.2357 --
obs0.2388 12037 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.948 Å2 / ksol: 0.253 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--35.9506 Å29.8252 Å210.3279 Å2
2---43.4632 Å2-5.4903 Å2
3----33.124 Å2
Refinement stepCycle: LAST / Resolution: 3→45.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 15 0 3743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043847
X-RAY DIFFRACTIONf_angle_d0.6975229
X-RAY DIFFRACTIONf_dihedral_angle_d16.2211376
X-RAY DIFFRACTIONf_chiral_restr0.045574
X-RAY DIFFRACTIONf_plane_restr0.003686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30180.39631260.31752789X-RAY DIFFRACTION96
3.3018-3.77940.33361430.26442925X-RAY DIFFRACTION98
3.7794-4.76090.27151590.21232853X-RAY DIFFRACTION98
4.7609-45.92280.27111660.20252876X-RAY DIFFRACTION98
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)
14.5704-0.9017-1.27845.0348-0.2896.6082-0.0014-0.58090.40260.90730.0392-0.1332-0.6171-0.0572-0.00040.9942-0.0506-0.05330.82270.03220.9079-46.63965.574716.2097
21.7424-1.565-0.89962.51791.09520.9584-0.17990.1761-0.12810.09380.2082-0.00750.31810.1621-0.00011.08170.03610.00541.18610.04481.0386-5.611612.4873-16.5074
33.2256-1.71220.69321.2657-0.16422.5739-0.1149-0.30770.0606-0.1193-0.10640.1562-0.3783-0.7822-01.5296-0.14780.071.6056-0.12391.13042.3005-48.6183-42.0043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A) AND (RESID 26:200 OR RESID 1530)
2X-RAY DIFFRACTION2(CHAIN A) AND (RESID 201:435 OR RESID 1531)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 436:529)

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