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Open data
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Basic information
Entry | Database: PDB / ID: 3fl7 | ||||||
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Title | Crystal structure of the human ephrin A2 ectodomain | ||||||
![]() | Ephrin receptor | ||||||
![]() | TRANSFERASE / SIGNALING PROTEIN / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / PHOSPHORYLATION / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / GLYCOPROTEIN / LIGAND BINDING DOMAIN / CYSTEINE-RICH DOMAIN / SUSHI DOMAIN / EGF-LIKE MOTIF / FIBRONECTIN DOMAIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / Membrane / Phosphoprotein | ||||||
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 / multicellular organism development / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly ...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 / multicellular organism development / 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 / positive regulation of kinase activity / 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 / plasma membrane => GO:0005886 / 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 / cell surface receptor protein tyrosine kinase signaling pathway / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / 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 / neuron projection / phosphorylation / focal adhesion / dendrite / cell surface / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walker, J.R. / Yermekbayeva, L. / Seitova, A. / Butler-Cole, C. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Architecture of Eph receptor clusters. Authors: Himanen, J.P. / Yermekbayeva, L. / Janes, P.W. / Walker, J.R. / Xu, K. / Atapattu, L. / Rajashankar, K.R. / Mensinga, A. / Lackmann, M. / Nikolov, D.B. / Dhe-Paganon, S. #1: Journal: J.Cell Biol. / Year: 2004 Title: Recruitment of Eph receptors into signaling clusters does not require ephrin contact. Authors: Wimmer-Kleikamp, S.H. / Janes, P.W. / Squire, A. / Bastiaens, P.I. / Lackmann, M. #2: Journal: J.Biol.Chem. / Year: 1998 Title: Distinct subdomains of the EphA3 receptor mediate ligand binding and receptor dimerization. Authors: Lackmann, M. / Oates, A.C. / Dottori, M. / Smith, F.M. / Do, C. / Power, M. / Kravets, L. / Boyd, A.W. #3: ![]() Title: Crystal structure of an Eph receptor-ephrin complex. Authors: Himanen, J.P. / Rajashankar, K.R. / Lackmann, M. / Cowan, C.A. / Henkemeyer, M. / Nikolov, D.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 | ![]() | 202.4 KB | Display | ![]() |
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PDB format | ![]() | 161.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.9 KB | Display | ![]() |
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Full document | ![]() | 463.7 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c8xSC ![]() 3czuC ![]() 3mbwC ![]() 3mx0C ![]() 2e7hS 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: 59218.930 Da / Num. of mol.: 1 / Fragment: Ectodomain, UNP residues 23-531 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N3Z2, UniProt: P29317*PLUS, receptor protein-tyrosine kinase | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | #4: Sugar | ChemComp-NAG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.03 % |
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Crystal grow | Temperature: 290.9 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 3.0% PEG 4000, 0.1M Sodium acetate, 0.1 M Cacodylate pH 5.5, 0.5 M NDSB 256, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2008 / Details: Mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→41 Å / Num. obs: 25966 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.07 / Net I/σ(I): 22.43 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.94 / Num. unique all: 2510 / Rsym value: 0.375 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 3C8X, 2E7H Resolution: 2.5→40.59 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.895 / SU B: 25.979 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.468 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 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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