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- PDB-4i1b: FUNCTIONAL IMPLICATIONS OF INTERLEUKIN-1BETA BASED ON THE THREE-D... -

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Basic information

Entry
Database: PDB / ID: 4i1b
TitleFUNCTIONAL IMPLICATIONS OF INTERLEUKIN-1BETA BASED ON THE THREE-DIMENSIONAL STRUCTURE
ComponentsINTERLEUKIN-1 BETA
KeywordsCYTOKINE
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 / negative regulation of cell population proliferation
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)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsVeerapandian, B. / Poulos, T.L. / Gilliland, G.L. / Raag, R. / Svensson, L.A. / Masui, Y. / Hirai, Y.
Citation
Journal: Proteins / Year: 1992
Title: Functional implications of interleukin-1 beta based on the three-dimensional structure.
Authors: Veerapandian, B. / Gilliland, G.L. / Raag, R. / Svensson, A.L. / Masui, Y. / Hirai, Y. / Poulos, T.L.
#1: Journal: J.Biol.Chem. / Year: 1987
Title: A Preliminary Crystallographic Study of Recombinant Human Interleukin 1Beta
Authors: Gilliland, G.L. / Winborne, E.L. / Masui, Y. / Hirai, Y.
History
DepositionMar 27, 1990Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-1 BETA


Theoretical massNumber of molelcules
Total (without water)17,3961
Polymers17,3961
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.140, 55.140, 76.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Atom site foot note1: RESIDUE PRO 91 IS A CIS PROLINE.

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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.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal grow
*PLUS
Method: other
Details: Gilliland, G.L., (1987) J. Biol. Chem., 262, 12323.

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. all: 14207 / Num. obs: 11013 / Observed criterion σ(I): 2 / Num. measured all: 25706 / Rmerge(I) obs: 0.05

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.19 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 0 91 1298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.039
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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