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- PDB-3mbw: Crystal structure of the human ephrin A2 LBD and CRD domains in c... -
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Basic information
Entry | Database: PDB / ID: 3mbw | |||||||||
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Title | Crystal structure of the human ephrin A2 LBD and CRD domains in complex with ephrin A1 | |||||||||
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![]() | TRANSFERASE/SIGNALING PROTEIN / ATP-binding / kinase / nucleotide-binding / receptor / transferase / phosphorylation / transmembrane / tyrosine-protein kinase / glycoprotein / cysteine-rich domain / phosphoprotein / GPI-anchor / lipoprotein / transferase-signaling protein complex / Structural Genomics Consortium / SGC | |||||||||
Function / homology | ![]() 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 / mitral valve morphogenesis / notochord cell development / 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 / mitral valve morphogenesis / 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 / negative regulation of epithelial to mesenchymal transition / tight junction / negative regulation of thymocyte apoptotic process / activation of GTPase activity / aortic valve morphogenesis / 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 / negative regulation of MAPK cascade / RHOV GTPase cycle / positive regulation of amyloid-beta formation / regulation of axonogenesis / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / positive regulation of protein tyrosine kinase activity / 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 / side of membrane / regulation of peptidyl-tyrosine phosphorylation / keratinocyte differentiation / RAC1 GTPase cycle / ephrin receptor binding / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / substrate adhesion-dependent cell spreading / 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 / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / lamellipodium / cell-cell signaling / virus receptor activity / angiogenesis / positive regulation of MAPK cascade / receptor complex / protein stabilization / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / positive regulation of protein phosphorylation / phosphorylation / focal adhesion / signaling receptor binding / dendrite / negative regulation of transcription by RNA polymerase II / cell surface / extracellular region / 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.1 KB | Display | ![]() |
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PDB format | ![]() | 147.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775 KB | Display | ![]() |
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Full document | ![]() | 781.3 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c8xSC ![]() 3czuC ![]() 3fl7C ![]() 3mx0C ![]() 1shwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36587.008 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P29317, receptor protein-tyrosine kinase |
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#2: Protein | Mass: 21398.688 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Chemical | ChemComp-UNX / |
#5: Water | ChemComp-HOH / |
Sequence details | STATE THAT THE CORRECT SEQUENCE IS PROVIDED IN GENBANK ENTRY NP_004422 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 290.9 K / pH: 8 Details: 10.0% PEG 3350, 0.16M AMMONIUM PHOSPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2008 |
Radiation | Monochromator: DOUBLE-CRYSTAL SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98792 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→39 Å / Num. obs: 16953 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 83.52 Å2 / Rsym value: 0.066 / Net I/σ(I): 23.65 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.17 / Rsym value: 0.668 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3C8X, 1SHW Resolution: 2.81→34.1 Å / Cor.coef. Fo:Fc: 0.9127 / Cor.coef. Fo:Fc free: 0.8839 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 80.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.551 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→34.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→3 Å / Total num. of bins used: 8
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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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