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Yorodumi- PDB-1bcn: THREE-DIMENSIONAL SOLUTION STRUCTURE OF HUMAN INTERLEUKIN-4 BY MU... -
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-Basic information
Entry | Database: PDB / ID: 1bcn | ||||||
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Title | THREE-DIMENSIONAL SOLUTION STRUCTURE OF HUMAN INTERLEUKIN-4 BY MULTI-DIMENSIONAL HETERONUCLEAR MAGNETIC RESONANCE SPECTROSCOPY | ||||||
Components | INTERLEUKIN-4 | ||||||
Keywords | CYTOKINE | ||||||
Function / homology | Function and homology information positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling ...positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / negative regulation of T-helper 17 cell differentiation / dendritic cell differentiation / positive regulation of T-helper 2 cell cytokine production / positive regulation of isotype switching to IgG isotypes / neuroinflammatory response / interleukin-4-mediated signaling pathway / macrophage activation / positive regulation of interleukin-13 production / myeloid dendritic cell differentiation / positive regulation of mast cell degranulation / regulation of phosphorylation / positive regulation of mononuclear cell migration / positive regulation of amyloid-beta clearance / type 2 immune response / activation of Janus kinase activity / positive regulation of MHC class II biosynthetic process / T-helper 2 cell differentiation / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of myoblast fusion / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / negative regulation of acute inflammatory response / positive regulation of interleukin-10 production / positive regulation of macroautophagy / negative regulation of tumor necrosis factor production / regulation of immune response / negative regulation of endothelial cell apoptotic process / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of defense response to virus by host / T cell activation / cholesterol metabolic process / B cell differentiation / innate immune response in mucosa / cytokine activity / negative regulation of extrinsic apoptotic signaling pathway / microglial cell activation / growth factor activity / negative regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of cell migration / immune response / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR | ||||||
Authors | Clore, G.M. / Powers, B. / Garrett, D.S. / Gronenborn, A.M. | ||||||
Citation | Journal: Science / Year: 1992 Title: Three-dimensional solution structure of human interleukin-4 by multidimensional heteronuclear magnetic resonance spectroscopy. Authors: Powers, R. / Garrett, D.S. / March, C.J. / Frieden, E.A. / Gronenborn, A.M. / Clore, G.M. #1: Journal: Science / Year: 1992 Title: Three-Dimensional Solution Structure of Human Interleukin-4 by Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Authors: Powers, R. / Garrett, D.S. / March, C.J. / Frieden, E.A. / Gronenborn, A.M. / Clore, G.M. #2: Journal: Biochemistry / Year: 1992 Title: 1H, 15N, 13C and 13Co Assignments of Human Interleukin-4 Using Three-Dimensional Double-and Triple-Resonance Heteronuclear Magnetic Resonance Spectroscopy Authors: Powers, R. / Garrett, D.S. / March, C.J. / Frieden, E.A. / Gronenborn, A.M. / Clore, G.M. #3: Journal: Biochemistry / Year: 1992 Title: Determination of the Secondary Structure and Folding Topology of Human Interleukin-4 Using Three-Dimensional Heteronuclear Magnetic Resonance Spectroscopy Authors: Garrett, D.S. / Powers, R. / March, C.J. / Frieden, E.A. / Clore, G.M. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bcn.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1bcn.ent.gz | 871.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bcn_validation.pdf.gz | 341.9 KB | Display | wwPDB validaton report |
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Full document | 1bcn_full_validation.pdf.gz | 538.7 KB | Display | |
Data in XML | 1bcn_validation.xml.gz | 55.3 KB | Display | |
Data in CIF | 1bcn_validation.cif.gz | 77.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/1bcn ftp://data.pdbj.org/pub/pdb/validation_reports/bc/1bcn | HTTPS FTP |
-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: 15391.601 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POTENTIAL / References: UniProt: P05112 |
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Sequence details | THE NUMBERING SCHEME IN THIS STRUCTURE INCLUDES THE FOUR-RESIDUE SEQUENCE GLU-ALA-GLU-ALA AT THE N- ...THE NUMBERING SCHEME IN THIS STRUCTURE INCLUDES THE FOUR-RESIDUE SEQUENCE GLU-ALA-GLU-ALA AT THE N-TERMINUS OF THE RECOMBINAN |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
Refinement | Software ordinal: 1 Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN REFERENCE 1 (I.E. AGREEMENT WITH EXPERIMENTAL RESTRAINTS, DEVIATIONS FROM IDEALITY FOR BOND LENGTHS, ANGLES, ...Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN REFERENCE 1 (I.E. AGREEMENT WITH EXPERIMENTAL RESTRAINTS, DEVIATIONS FROM IDEALITY FOR BOND LENGTHS, ANGLES, PLANES AND CHIRALITY, NON-BONDED CONTACTS, ATOMIC RMS DIFFERENCES BETWEEN THE CALCULATED STRUCTURES. THE STRUCTURES ARE BASED ON 823 INTERPROTON DISTANCE RESTRAINTS FROM NOE MEASUREMENTS; 98 HYDROGEN-BONDING DISTANCE RESTRAINTS FOR 49 HYDROGEN-BONDS IDENTIFIED ON THE BASIS OF THE NOE AND AMIDE PROTON EXCHANGE DATA, AS WELL AS THE INITIAL STRUCTURE CALCULATIONS; AND 101 PHI AND 82 PSI BACKBONE TORSION ANGLE RESTRAINTS DERIVED FROM COUPLING CONSTANTS, NOE DATA, AND 13C SECONDARY CHEMICAL SHIFTS. THE METHOD USED TO DETERMINE THE STRUCTURES IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M. NILGES, G. M. CLORE, AND A. M. GRONENBORN FEBS LETT. 229, 317-324 (1988)). RESIDUES 1 - 6 AND 132 - 133 AT THE N- AND C-TERMINI ARE DISORDERED. THE RESTRAINED MINIMIZED AVERAGE STRUCTURE IS PRESENTED IN PROTEIN DATA BANK ENTRY 1BBN. THIS WAS OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. MODELS 1 - 22, PRESENTED IN THIS ENTRY, REPRESENT THE INDIVIDUAL MODELS. THE (SA)R RESTRAINED MINIMIZED MEAN STRUCTURE WAS DERIVED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL SA STRUCTURES (BEST FITTED TO RESIDUES 7 - 131), AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 IN ENTRY 1BBN REPRESENTS THE ATOMIC RMS DEVIATIONS OF THE 22 INDIVIDUAL SA STRUCTURES ABOUT THE MEAN STRUCTURE. |
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NMR ensemble | Conformers submitted total number: 22 |