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Yorodumi- PDB-7i1b: HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN-1 BETA... -
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-Basic information
Entry | Database: PDB / ID: 7i1b | ||||||
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Title | HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN-1 BETA IN SOLUTION BY THREE-AND FOUR-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY | ||||||
Components | INTERLEUKIN-1 BETA | ||||||
Keywords | CYTOKINE | ||||||
Function / homology | Function and homology information smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / cellular response to interleukin-17 / sequestering of triglyceride / positive regulation of RNA biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / neutrophil activation / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of monocyte chemotactic protein-1 production / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of heterotypic cell-cell adhesion / negative regulation of synaptic transmission / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / positive regulation of granulocyte macrophage colony-stimulating factor production / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / response to ATP / : / macrophage chemotaxis / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cell division / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / ectopic germ cell programmed cell death / Pyroptosis / negative regulation of lipid catabolic process / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / positive regulation of glial cell proliferation / JNK cascade / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / embryo implantation / response to interleukin-1 / positive regulation of mitotic nuclear division / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / positive regulation of protein export from nucleus / negative regulation of MAP kinase activity / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis / Interleukin-1 signaling / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of angiogenesis / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / integrin binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / immune response / protein domain specific binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR | ||||||
Authors | Clore, G.M. / Gronenborn, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 1991 Title: High-resolution three-dimensional structure of interleukin 1 beta in solution by three- and four-dimensional nuclear magnetic resonance spectroscopy. Authors: Clore, G.M. / Wingfield, P.T. / Gronenborn, A.M. #1: Journal: Biochemistry / Year: 1991 Title: Four-Dimensional 13C(Slash)13C-Edited Nuclear Overhauser Enhancement Spectroscopy of a Protein in Solution: Application to Interleukin-1Beta Authors: Clore, G.M. / Kay, L.E. / Bax, A. / Gronenborn, A.M. #2: Journal: Science / Year: 1990 Title: Four-Dimensional Heteronuclear Triple-Resonance NMR Spectroscopy of Interleukin-1Beta in Solution Authors: Kay, L.E. / Clore, G.M. / Bax, A. / Gronenborn, A.M. #3: Journal: Biochemistry / Year: 1990 Title: Assignment of the Side-Chain 1H and 13C Resonances of Interleukin-1Beta Using Double-and Triple-Resonance Heteronuclear Three-Dimensional NMR Spectroscopy Authors: Clore, G.M. / Bax, A. / Driscoll, P.C. / Wingfield, P.T. / Gronenborn, A.M. #4: Journal: Biochemistry / Year: 1990 Title: Analysis of the Backbone Dynamics of Interleukin-1Beta Using Two-Dimensional Inverse Detected Heteronuclear 15N-1H NMR Spectroscopy Authors: Clore, G.M. / Driscoll, P.C. / Wingfield, P.T. / Gronenborn, A.M. #5: Journal: Biochemistry / Year: 1990 Title: Identification and Localization of Bound Internal Water in the Solution Structure of Interleukin 1Beta by Heteronuclear Three-Dimensional 1H Rotating-Frame Overhauser 15N-1H Multiple Quantum ...Title: Identification and Localization of Bound Internal Water in the Solution Structure of Interleukin 1Beta by Heteronuclear Three-Dimensional 1H Rotating-Frame Overhauser 15N-1H Multiple Quantum Coherence NMR Spectroscopy Authors: Clore, G.M. / Bax, A. / Wingfield, P.T. / Gronenborn, A.M. #6: Journal: J.Mol.Biol. / Year: 1990 Title: Low Resolution Structure of Interleukin-1Beta in Solution Derived from 1H-15N Heteronuclear Three-Dimensional Nuclear Magnetic Resonance Spectroscopy Authors: Clore, G.M. / Driscoll, P.C. / Wingfield, P.T. / Gronenborn, A.M. #7: Journal: Biochemistry / Year: 1990 Title: Determination of the Secondary Structure and Molecular Topology of Interleukin-1Beta by Use of Two-and Three-Dimensional Heteronuclear 15N-1H NMR Spectroscopy Authors: Driscoll, P.C. / Gronenborn, A.M. / Wingfield, P.T. / Clore, G.M. #8: Journal: Biochemistry / Year: 1990 Title: Complete Resonance Assignment for the Polypeptide Backbone of Interleukin 1Beta Using Three-Dimensional Heteronuclear NMR Spectroscopy Authors: Driscoll, P.C. / Clore, G.M. / Marion, D. / Wingfield, P.T. / Gronenborn, A.M. #9: Journal: Biochemistry / Year: 1989 Title: Overcoming the Overlap Problem in the Assignment of 1H NMR Spectra of Larger Proteins by Use of Three-Dimensional Heteronuclear 1H-15N Hartmann-Hahn-Multiple Quantum Coherence and Nuclear ...Title: Overcoming the Overlap Problem in the Assignment of 1H NMR Spectra of Larger Proteins by Use of Three-Dimensional Heteronuclear 1H-15N Hartmann-Hahn-Multiple Quantum Coherence and Nuclear Overhauser-Multiple Quantum Coherence Spectroscopy: Application to Interleukin 1Beta Authors: Marion, D. / Driscoll, P.C. / Kay, L.E. / Wingfield, P.T. / Bax, A. / Gronenborn, A.M. / Clore, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 7i1b.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7i1b.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 7i1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7i1b_validation.pdf.gz | 353.5 KB | Display | wwPDB validaton report |
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Full document | 7i1b_full_validation.pdf.gz | 598.6 KB | Display | |
Data in XML | 7i1b_validation.xml.gz | 117 KB | Display | |
Data in CIF | 7i1b_validation.cif.gz | 146.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/7i1b ftp://data.pdbj.org/pub/pdb/validation_reports/i1/7i1b | HTTPS FTP |
-Related structure data
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-Assembly
Deposited unit |
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1 |
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Atom site foot note | 1: RESIDUE 91 IS A CIS PROLINE. | |||||||||
NMR ensembles |
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-Components
#1: Protein | Mass: 17395.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01584 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Processing
Refinement | Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON 2630 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 114 HYDROGEN BONDING DISTANCE RESTRAINTS FOR 57 HYDROGEN-BONDS IDENTIFIED ON THE BASIS OF THE ...Details: THE STRUCTURES ARE BASED ON 2630 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 114 HYDROGEN BONDING DISTANCE RESTRAINTS FOR 57 HYDROGEN-BONDS IDENTIFIED ON THE BASIS OF THE NOE AND AMIDE PROTON EXCHANGE DATA, AS WELL AS THE INITIAL STRUCTURE CALCULATIONS; 36 DISTANCE RESTRAINTS RELATING TO NH-H2O-CO BRIDGING HYDROGEN BONDS INVOLVING 7 BOUND WATER MOLECULES AND IDENTIFIED FROM ROE MEASUREMENTS; AND 152 PHI AND 115 PSI BACKBONE TORSION ANGLE RESTRAINTS AND 99 CHI SIDE CHAIN TORSION ANGLE RESTRAINTS DERIVED FROM COUPLING CONSTRAINTS AND NOE DATA. THE LATTER ARE OBTAINED USING THE CONFORMATIONAL GRID SEARCH PROGRAM "STEREOSEARCH" (M. NILGES, G. M. CLORE, AND A. M. GRONENBORN (1990) BIOPOLYMERS 29, 813-822). 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, (1990) FEBS LETT. 229, 317-324). THE QUANTITY PRESENTED IN THE B-VALUE FIELD IN THIS COORDINATE FILE REPRESENTS THE ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. THE RESTRAINED MINIMIZED AVERAGE STRUCTURE CAN BE FOUND IN PDB ENTRY 6I1B. IT WAS OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. |
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NMR ensemble | Conformers submitted total number: 32 |