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- PDB-6i1b: HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN-1 BETA... -

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Entry
Database: PDB / ID: 6i1b
TitleHIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN-1 BETA IN SOLUTION BY THREE-AND FOUR-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
ComponentsINTERLEUKIN-1 BETA
KeywordsCYTOKINE
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / : / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / positive regulation of tight junction disassembly / positive regulation of prostaglandin biosynthetic process / negative regulation of gap junction assembly / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of prostaglandin secretion / positive regulation of neuroinflammatory response / positive regulation of platelet-derived growth factor receptor signaling pathway / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / regulation of establishment of endothelial barrier / CLEC7A/inflammasome pathway / Interleukin-1 processing / negative regulation of synaptic transmission / response to carbohydrate / positive regulation of monocyte chemotactic protein-1 production / interleukin-1 receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of p38MAPK cascade / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of cell division / regulation of neurogenesis / positive regulation of vascular endothelial growth factor production / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of MAP kinase activity / Pyroptosis / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / JNK cascade / positive regulation of glial cell proliferation / neutrophil chemotaxis / embryo implantation / negative regulation of insulin receptor signaling pathway / positive regulation of interleukin-2 production / response to interleukin-1 / positive regulation of mitotic nuclear division / regulation of insulin secretion / secretory granule / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / cytokine-mediated signaling pathway / negative regulation of neurogenesis / positive regulation of interleukin-6 production / positive regulation of type II interferon production / Interleukin-1 signaling / cellular response to mechanical stimulus / positive regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of NF-kappaB transcription factor activity / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / protein domain specific binding / negative regulation of cell population proliferation / apoptotic process
Similarity search - Function
Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsClore, 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
DepositionJan 22, 1991Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN-1 BETA


Theoretical massNumber of molelcules
Total (without water)17,3961
Polymers17,3961
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: RESIDUE 91 IS A CIS PROLINE.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein INTERLEUKIN-1 BETA


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

RefinementSoftware 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). A TOTAL OF 32 STRUCTURES WERE CALCULATED. THIS ENTRY REPRESENTS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE. IT WAS OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. 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.
NMR ensembleConformers submitted total number: 1

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