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- PDB-7kjb: Crystal structure of the EphA2 S897E/S901E mutant intracellular K... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kjb | ||||||
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Title | Crystal structure of the EphA2 S897E/S901E mutant intracellular KD-SAM domains | ||||||
![]() | Ephrin type-A receptor 2 | ||||||
![]() | TRANSFERASE / Eph receptor / kinase / SAM / allostery | ||||||
Function / homology | ![]() 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 / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / transmembrane-ephrin receptor activity / response to growth factor / tight junction / activation of GTPase activity / 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of ERK1 and ERK2 cascade / 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 / axon guidance / receptor protein-tyrosine kinase / ruffle membrane / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / virus receptor activity / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / phosphorylation / focal adhesion / dendrite / cell surface / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lechtenberg, B.C. / Pasquale, E.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Regulation of the EphA2 receptor intracellular region by phosphomimetic negative charges in the kinase-SAM linker. Authors: Lechtenberg, B.C. / Gehring, M.P. / Light, T.P. / Horne, C.R. / Matsumoto, M.W. / Hristova, K. / Pasquale, E.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.9 KB | Display | ![]() |
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PDB format | ![]() | 182 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.4 KB | Display | ![]() |
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Full document | ![]() | 422.4 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kjaC ![]() 7kjcC ![]() 3kkaS ![]() 4pdoS S: Starting model for refinement C: citing same article ( |
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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: 44042.691 Da / Num. of mol.: 1 / Mutation: S897E, S901E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P29317, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-CS / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.78 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 4.5% Tacsimate, 0.09 M HEPES pH 7.0, 9% PEG-MME 5K, 0.1 M CsCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.53 Å / Num. obs: 13051 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 50.49 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.285 / Rpim(I) all: 0.13 / Rrim(I) all: 0.313 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 11 % / Rmerge(I) obs: 1.956 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1871 / CC1/2: 0.554 / Rpim(I) all: 0.895 / Rrim(I) all: 2.153 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PDO, 3KKA Resolution: 2.8→29.53 Å / SU ML: 0.3866 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7528 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→29.53 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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