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Yorodumi- PDB-3mbw: Crystal structure of the human ephrin A2 LBD and CRD domains in c... -
+Open data
-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 | |||||||||
Components |
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Keywords | 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 | 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 chemokine production / ephrin receptor activity / negative regulation of epithelial to mesenchymal transition / leading edge membrane / bone remodeling / post-anal tail morphogenesis / response to growth factor / activation of GTPase activity / negative regulation of thymocyte apoptotic process / regulation of lamellipodium assembly / aortic valve morphogenesis / 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 / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / positive regulation of protein tyrosine kinase activity / 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 / cell migration / positive regulation of peptidyl-tyrosine phosphorylation / 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 / Resolution: 2.81 Å | |||||||||
Authors | 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) | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mbw.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mbw.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/3mbw ftp://data.pdbj.org/pub/pdb/validation_reports/mb/3mbw | HTTPS FTP |
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-Related structure data
Related structure data | 3c8xSC 3czuC 3fl7C 3mx0C 1shwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: ECK, EPHA2 / Plasmid: PFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 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.) Homo sapiens (human) / Gene: EFNA1, EPLG1, LERK1, TNFAIP4 / Plasmid: PFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P20827 |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98792 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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