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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 | ||||||
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Title | Crystal structure of the complete EphA2 ectodomain in complex with ephrin A5 receptor binding domain | ||||||
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![]() | RECEPTOR/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 | ![]() neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / negative regulation of substrate adhesion-dependent cell spreading / regulation of cell-cell adhesion / notochord cell development / synaptic membrane adhesion / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis ...neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / negative regulation of substrate adhesion-dependent cell spreading / regulation of cell-cell adhesion / notochord cell development / synaptic membrane adhesion / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / cellular response to follicle-stimulating hormone stimulus / pericyte cell differentiation / collateral sprouting / cAMP metabolic process / positive regulation of bicellular tight junction assembly / positive regulation of collateral sprouting / regulation of blood vessel endothelial cell migration / ephrin receptor activity / regulation of insulin secretion involved in cellular response to glucose stimulus / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / chemorepellent activity / neurotrophin TRKA receptor binding / response to growth factor / regulation of cell morphogenesis / tight junction / activation of GTPase activity / positive regulation of synapse assembly / 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 / regulation of focal adhesion assembly / RHOV GTPase cycle / retinal ganglion cell axon guidance / regulation of GTPase activity / EPHA-mediated growth cone collapse / transmembrane receptor protein tyrosine kinase activator activity / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / basement membrane / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / GABA-ergic synapse / RAC3 GTPase cycle / vasculogenesis / regulation of angiogenesis / regulation of microtubule cytoskeleton organization / keratinocyte differentiation / cellular response to forskolin / RAC1 GTPase cycle / ephrin receptor binding / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / caveola / axon guidance / protein localization to plasma membrane / cell motility / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / adherens junction / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / positive regulation of peptidyl-tyrosine phosphorylation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / virus receptor activity / nervous system development / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / cadherin binding / positive regulation of protein phosphorylation / external side of plasma membrane / focal adhesion / cell surface / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seiradake, E. / Harlos, K. / Sutton, G. / Aricescu, A.R. / Jones, E.Y. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 261.3 KB | Display | ![]() |
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PDB format | ![]() | 213.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2x10C ![]() 1shwS ![]() 3czuS ![]() 3fl7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | 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.) ![]() ![]() References: UniProt: P29317, receptor protein-tyrosine kinase |
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#2: Protein | 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.) ![]() ![]() |
Sequence details | CONTAINS FOREIGN SIGNAL PEPTIDE AND POLY-HIS TAG |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | Details: 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. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 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.
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Solvent computation | Shrinkage 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 |
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Refinement step | Cycle: LAST / Resolution: 4.83→40.482 Å
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Refine LS restraints |
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LS refinement shell |
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