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Yorodumi- PDB-2eot: SOLUTION STRUCTURE OF EOTAXIN, AN ENSEMBLE OF 32 NMR SOLUTION STR... -
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-Basic information
Entry | Database: PDB / ID: 2eot | ||||||
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Title | SOLUTION STRUCTURE OF EOTAXIN, AN ENSEMBLE OF 32 NMR SOLUTION STRUCTURES | ||||||
Components | EOTAXIN | ||||||
Keywords | CYTOKINE / CHEMOKINE / PROTEIN SYNTHESIS / EOTAXIN / SOLUTION STRUCTURE / CCR3 / EOSINOPHIL | ||||||
Function / homology | Function and homology information response to interleukin-13 / CCR3 chemokine receptor binding / chronic inflammatory response / response to interleukin-4 / mast cell chemotaxis / mammary duct terminal end bud growth / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway ...response to interleukin-13 / CCR3 chemokine receptor binding / chronic inflammatory response / response to interleukin-4 / mast cell chemotaxis / mammary duct terminal end bud growth / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / branching involved in mammary gland duct morphogenesis / chemokine activity / positive regulation of actin filament polymerization / monocyte chemotaxis / cellular response to interleukin-1 / cytoskeleton organization / ERK1 and ERK2 cascade / positive regulation of endothelial cell proliferation / neutrophil chemotaxis / actin filament organization / response to virus / response to radiation / intracellular calcium ion homeostasis / positive regulation of GTPase activity / cellular response to type II interferon / negative regulation of neurogenesis / positive regulation of angiogenesis / chemotaxis / cellular response to tumor necrosis factor / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / learning or memory / protein dimerization activity / cell adhesion / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / signal transduction / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Crump, M.P. / Rajarathnam, K. / Kim, K.-S. / Clark-Lewis, I. / Sykes, B.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Solution structure of eotaxin, a chemokine that selectively recruits eosinophils in allergic inflammation. Authors: Crump, M.P. / Rajarathnam, K. / Kim, K.S. / Clark-Lewis, I. / Sykes, B.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eot.cif.gz | 829.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eot.ent.gz | 732.6 KB | Display | PDB format |
PDBx/mmJSON format | 2eot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/2eot ftp://data.pdbj.org/pub/pdb/validation_reports/eo/2eot | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8380.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: BOTH SYNTHETIC AND RECOMBINANT SAMPLES WERE PREPARED YES Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P51671 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 90% H2O/10% H2O OR 100% D2O BUFFER, ALSO CONTAINED 1MM DSS AND 1MM SODIUM AZIDE |
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Sample conditions | Ionic strength: 20mM SODIUM ACETATE / pH: 5.00 / Pressure: 1 atm / Temperature: 303 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
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NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: STRUCTURES WERE REFINED WITH MULTIPLE ROUNDS OF SIMULATED ANNEALING WITH THE ADDITION OF NEW NOES AND CORRECTION OF UNAMBIGUOUS NOES. PHI ANGLES WERE ONLY ADDED WHEN THEY AGREED WITH THE ...Details: STRUCTURES WERE REFINED WITH MULTIPLE ROUNDS OF SIMULATED ANNEALING WITH THE ADDITION OF NEW NOES AND CORRECTION OF UNAMBIGUOUS NOES. PHI ANGLES WERE ONLY ADDED WHEN THEY AGREED WITH THE PURELY NOE DRIVEN CONVERGENCE OF THAT ANGLE IN INITIAL STRUCTURE CALCULATIONS. OTHER REFINEMENT INFORMATION CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WERE SELECTED WITH NO VIOLATIONS GREATER THAN 0.3 ANGSTROMS OR DIHEDRAL ANGLES GREATER THAN 0.5 ANGSTROMS AND GOOD COVALENT GEOMETRY. Conformers calculated total number: 40 / Conformers submitted total number: 32 |