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- PDB-2mib: THE STRUCTURE OF MURINE INTERLEUKIN-1 BETA AT 2.8 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2mib
TitleTHE STRUCTURE OF MURINE INTERLEUKIN-1 BETA AT 2.8 ANGSTROMS RESOLUTION
ComponentsINTERLEUKIN-1 BETA
KeywordsCYTOKINE
Function / homology
Function and homology information


CLEC7A/inflammasome pathway / Pyroptosis / Interleukin-1 processing / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...CLEC7A/inflammasome pathway / Pyroptosis / Interleukin-1 processing / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / 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 / Interleukin-1 signaling / positive regulation of complement activation / cellular response to interleukin-17 / positive regulation of tight junction disassembly / positive regulation of prostaglandin biosynthetic process / negative regulation of gap junction assembly / vascular endothelial growth factor production / positive regulation of prostaglandin secretion / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / regulation of establishment of endothelial barrier / 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 granulocyte macrophage colony-stimulating factor production / interleukin-1-mediated signaling pathway / leukocyte migration / response to ATP / positive regulation of cell division / 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 / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of chemokine production / JNK cascade / positive regulation of glial cell proliferation / neutrophil chemotaxis / negative regulation of insulin receptor signaling pathway / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / regulation of insulin secretion / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of type II interferon production / cellular response to mechanical stimulus / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / vesicle / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / receptor ligand activity / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / cytosol
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.84 Å
AuthorsPriestle, J.P. / Van Oostrum, J. / Schmitz, A. / Gruetter, M.G.
CitationJournal: J.Struct.Biol. / Year: 1991
Title: The structure of murine interleukin-1 beta at 2.8 A resolution.
Authors: van Oostrum, J. / Priestle, J.P. / Grutter, M.G. / Schmitz, A.
History
DepositionDec 6, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA BARREL. ...SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)17,4161
Polymers17,4161
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.500, 55.500, 78.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Atom site foot note1: CIS PROLINE - PRO 91

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Components

#1: Protein INTERLEUKIN-1 BETA


Mass: 17415.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P10749
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS ALIGNED TO THE HUMAN INTERLEUKIN-1 BETA SEQUENCE. THIS RESULTS IN THE DELETION OF ...THE SEQUENCE IS ALIGNED TO THE HUMAN INTERLEUKIN-1 BETA SEQUENCE. THIS RESULTS IN THE DELETION OF RESIDUE 139 IN MURINE SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.59 %

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.84→10 Å / Rfactor obs: 0.173 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.84→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 0 42 1247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d1.6
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

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