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Yorodumi- PDB-3hei: Ligand Recognition by A-Class Eph Receptors: Crystal Structures o... -
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-Basic information
Entry | Database: PDB / ID: 3hei | ||||||
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Title | Ligand Recognition by A-Class Eph Receptors: Crystal Structures of the EphA2 Ligand-Binding Domain and the EphA2/ephrin-A1 Complex | ||||||
Components |
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Keywords | TRANSFERASE/SIGNALING PROTEIN / Eph receptor tyrosine kinase / ephrin / Cell membrane / Disulfide bond / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / TRANSFERASE-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information endocardial cushion to mesenchymal transition involved in heart valve formation / negative regulation of proteolysis involved in protein catabolic process / negative regulation of dendritic spine morphogenesis / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / notochord cell development / mitral valve morphogenesis / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis ...endocardial cushion to mesenchymal transition involved in heart valve formation / negative regulation of proteolysis involved in protein catabolic process / negative regulation of dendritic spine morphogenesis / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / notochord cell development / mitral valve morphogenesis / 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 / negative regulation of epithelial to mesenchymal transition / negative regulation of chemokine production / ephrin receptor activity / leading edge membrane / bone remodeling / post-anal tail morphogenesis / response to growth factor / activation of GTPase activity / aortic valve morphogenesis / regulation of lamellipodium assembly / negative regulation of thymocyte apoptotic process / tight junction / 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 / regulation of axonogenesis / positive regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / negative regulation of MAPK cascade / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / positive regulation of protein tyrosine kinase activity / vasculogenesis / regulation of angiogenesis / side of membrane / regulation of peptidyl-tyrosine phosphorylation / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / ephrin receptor binding / cell chemotaxis / negative regulation of angiogenesis / substrate adhesion-dependent cell spreading / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / skeletal system development / molecular function activator activity / cell motility / axon guidance / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / virus receptor activity / cell-cell signaling / lamellipodium / angiogenesis / positive regulation of MAPK cascade / protein stabilization / receptor complex / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / cadherin binding / inflammatory response / positive regulation of protein phosphorylation / phosphorylation / signaling receptor binding / focal adhesion / negative regulation of transcription by RNA polymerase II / cell surface / extracellular region / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Himanen, J.P. / Goldgur, Y. / Miao, H. / Myshkin, E. / Guo, H. / Buck, M. / Nguyen, M. / Rajashankar, K.R. / Wang, B. / Nikolov, D.B. | ||||||
Citation | Journal: Embo Rep. / Year: 2009 Title: Ligand recognition by A-class Eph receptors: crystal structures of the EphA2 ligand-binding domain and the EphA2/ephrin-A1 complex. Authors: Himanen, J.P. / Goldgur, Y. / Miao, H. / Myshkin, E. / Guo, H. / Buck, M. / Nguyen, M. / Rajashankar, K.R. / Wang, B. / Nikolov, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hei.cif.gz | 553.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hei.ent.gz | 468.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/3hei ftp://data.pdbj.org/pub/pdb/validation_reports/he/3hei | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 19913.592 Da / Num. of mol.: 8 / Fragment: UNP residues 28-201 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Plasmid: pBabe / Cell (production host): human embryonic kidney (HEK) cells / Cell line (production host): HEK293 / Organ (production host): kidney / Production host: HOMO SAPIENS (human) References: UniProt: P29317, receptor protein-tyrosine kinase #2: Protein | Mass: 15884.819 Da / Num. of mol.: 8 / Fragment: UNP residues 18-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EFNA1, EPLG1, LERK1, TNFAIP4 / Plasmid: pBabe / Cell (production host): human embryonic kidney (HEK) cells / Cell line (production host): HEK293 / Organ (production host): kidney / Production host: HOMO SAPIENS (human) / References: UniProt: P20827 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 8,000, 100 mM Tris, pH 8.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 192014 / % possible obs: 96.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.214 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | R rigid body: 0.391 / Cor.coef. Fo:Fc: 0.609 / Cor.coef. Io to Ic: 0.607 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.925 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.358 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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