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Yorodumi- PDB-3hpn: Ligand recognition by A-class EPH receptors: crystal structures o... -
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-Basic information
Entry | Database: PDB / ID: 3hpn | ||||||
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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 | Ephrin type-A receptor 2 | ||||||
Keywords | TRANSFERASE / Eph receptor tyrosine kinase / ephrin / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase | ||||||
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 / 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 / regulation of lamellipodium assembly / 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 / 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 / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / vasculogenesis / regulation of angiogenesis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / cell chemotaxis / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / skeletal system development / cell motility / molecular function activator activity / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / neuron differentiation / receptor protein-tyrosine kinase / osteoblast differentiation / ruffle membrane / cell surface receptor protein tyrosine kinase signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / virus receptor activity / lamellipodium / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / phosphorylation / focal adhesion / cell surface / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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 | 3hpn.cif.gz | 219.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hpn.ent.gz | 171.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpn ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpn | HTTPS FTP |
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-Related structure data
Related structure data | 3heiC 3etpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 3 / Auth seq-ID: 1 - 174 / Label seq-ID: 1 - 174
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-Components
#1: Protein | Mass: 19913.592 Da / Num. of mol.: 6 / 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 line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo Sapiens (human) References: UniProt: P29317, receptor protein-tyrosine kinase #2: 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: 2.43 Å3/Da / Density % sol: 49.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 4,000, 100 mM Tris, 100 mM Sodium Acetate, 3% ethylene glycol, 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: 2.5→30 Å / Num. all: 38120 / Num. obs: 36900 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.094 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.2 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ETP Resolution: 2.52→30 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.825 / Occupancy max: 1 / Occupancy min: 1 / SU B: 29.348 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / 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: 2.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.52→2.584 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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