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- PDB-8i1b: A COMPARISON OF THE HIGH RESOLUTION STRUCTURES OF HUMAN AND MURIN... -

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Entry
Database: PDB / ID: 8i1b
TitleA COMPARISON OF THE HIGH RESOLUTION STRUCTURES OF HUMAN AND MURINE INTERLEUKIN-1B
ComponentsINTERLEUKIN-1 BETA
KeywordsCYTOKINE
Function / homology
Function and homology information


CLEC7A/inflammasome pathway / CASP4-mediated substrate cleavage / CASP5-mediated substrate cleavage / interleukin-1 receptor complex / negative regulation of branching morphogenesis of a nerve / ectopic germ cell programmed cell death / Pyroptosis / positive regulation of glial cell differentiation / negative regulation of glutamate secretion / Interleukin-1 processing ...CLEC7A/inflammasome pathway / CASP4-mediated substrate cleavage / CASP5-mediated substrate cleavage / interleukin-1 receptor complex / negative regulation of branching morphogenesis of a nerve / ectopic germ cell programmed cell death / Pyroptosis / positive regulation of glial cell differentiation / negative regulation of glutamate secretion / Interleukin-1 processing / negative regulation of adiponectin secretion / negative regulation of neural precursor cell proliferation / negative regulation of lipid metabolic process / positive regulation of JUN kinase activity / negative regulation of D-glucose transmembrane transport / positive regulation of lipid catabolic process / positive regulation of stress-activated MAPK cascade / regulation of nitric-oxide synthase activity / positive regulation of T-helper 1 cell cytokine production / hyaluronan biosynthetic process / positive regulation of astrocyte differentiation / cellular response to interleukin-17 / positive regulation of complement activation / positive regulation of RNA biosynthetic process / monocyte aggregation / fever generation / positive regulation of tight junction disassembly / Interleukin-1 signaling / positive regulation of immature T cell proliferation in thymus / negative regulation of gap junction assembly / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of prostaglandin biosynthetic process / regulation of defense response to virus by host / positive regulation of platelet-derived growth factor receptor signaling pathway / response to carbohydrate / positive regulation of prostaglandin secretion / regulation of establishment of endothelial barrier / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of glial cell proliferation / positive regulation of monocyte chemotactic protein-1 production / positive regulation of macrophage derived foam cell differentiation / positive regulation of p38MAPK cascade / interleukin-1 receptor binding / negative regulation of synaptic transmission / positive regulation of heterotypic cell-cell adhesion / positive regulation of cell division / positive regulation of membrane protein ectodomain proteolysis / positive regulation of neutrophil chemotaxis / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / leukocyte migration / negative regulation of neuron differentiation / response to ATP / regulation of insulin secretion / extrinsic apoptotic signaling pathway in absence of ligand / social behavior / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / regulation of neurogenesis / positive regulation of epithelial to mesenchymal transition / regulation of ERK1 and ERK2 cascade / negative regulation of lipid catabolic process / neutrophil chemotaxis / negative regulation of MAPK cascade / positive regulation of chemokine production / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / positive regulation of mitotic nuclear division / astrocyte activation / cytokine activity / secretory granule / response to interleukin-1 / : / positive regulation of interleukin-8 production / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / memory / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of JNK cascade / negative regulation of neurogenesis / integrin binding / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / cytokine-mediated signaling pathway / positive regulation of angiogenesis / positive regulation of neuron apoptotic process / positive regulation of inflammatory response / response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vesicle / positive regulation of ERK1 and ERK2 cascade / inflammatory response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / defense response to Gram-positive bacterium
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: 2.4 Å
AuthorsOhlendorf, D.H. / Weber, P.C. / Salemme, F.R.
CitationJournal: To be Published
Title: A Comparison of the High Resolution Structures of Human and Murine Interleukin-1B
Authors: Ohlendorf, D.H. / Treharne, A.C. / Weber, P.C. / Wendoloski, J.J. / Salemme, F.R.
History
DepositionJan 29, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 14, 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 ARRANGEMENT OF THE STRANDS IN IL-1 MAKES A SHEET DESIGNATION MEANINGLESS. THE 12 STRANDS ...SHEET THE ARRANGEMENT OF THE STRANDS IN IL-1 MAKES A SHEET DESIGNATION MEANINGLESS. THE 12 STRANDS HAVE BEEN PRESENTED AS 12 SHEETS OF ONE STRAND EACH ON THE SHEET RECORDS BELOW. THE FIRST GROUP OF FOUR STRANDS ARE PART OF MOTIF A. THE SECOND GROUP OF FOUR STRANDS ARE PART OF MOTIF B. THE THIRD GROUP OF FOUR STRANDS ARE PART OF MOTIF C.

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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
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.710, 55.710, 79.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Atom site foot note1: PRO 91 IS A CIS PROLINE.
2: SOLVENT MOLECULES 201, 202 AND 204 COORDINATE THE INTERSECTIONS OF THREE BETA STRANDS.
3: GLN 14, ILE 36, LYS 93 AND VAL 110 SIDECHAINS HAVE BEEN MODELED IN TWO ALTERNATE CONFORMATIONS OF EQUAL OCCUPANCY.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.45441, -0.68838, 0.56537), (0.22777, 0.52379, 0.82083), (-0.86118, 0.50177, -0.08123)29.252, 7.638, -1.706
2given(-0.45441, 0.22777, -0.86118), (-0.68838, 0.52379, 0.50177), (0.56537, 0.82083, -0.08213)10.083, 16.992, -22.946

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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.: 86 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE MOLECULE CAN BE DIVIDED INTO THREE SIMILAR MOTIFS, (RESIDUES 1 - 55, RESIDUES 56 - 107, AND ...THE MOLECULE CAN BE DIVIDED INTO THREE SIMILAR MOTIFS, (RESIDUES 1 - 55, RESIDUES 56 - 107, AND RESIDUES 108 - 153). THESE MOTIFS ARE RELATED BY A LOCAL THREE-FOLD AXIS. THE TRANSFORMATION PRESENTED IN MTRIX 1 PRODUCES MOTIFS BCA FROM MOTIFS ABC. THE TRANSFORMATION PRESENTED IN MTRIX 2 PRODUCES MOTIFS CAB FROM MOTIFS ABC.
Nonpolymer detailsSOLVENT MOLECULES 201, 202 AND 204 COORDINATE THE INTERSECTIONS OF THREE BETA STRANDS.
Sequence detailsRESIDUES HAVE BEEN NUMBERED TO AGREE WITH HUMAN IL-1BETA. THIS MEANS THERE IS NO RESIDUE 140.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.03 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→5 Å /
RfactorNum. reflection
obs0.159 6771
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 0 86 1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.03
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0471
X-RAY DIFFRACTIONp_mcangle_it1.9172
X-RAY DIFFRACTIONp_scbond_it1.5211.5
X-RAY DIFFRACTIONp_scangle_it2.5513
X-RAY DIFFRACTIONp_plane_restr0.0150.03
X-RAY DIFFRACTIONp_chiral_restr0.260.3
X-RAY DIFFRACTIONp_singtor_nbd0.2170.5
X-RAY DIFFRACTIONp_multtor_nbd0.2530.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.220.5
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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