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- PDB-8c3u: Crystal Structure of human IL-1beta in complex with a low molecul... -

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Basic information

Entry
Database: PDB / ID: 8c3u
TitleCrystal Structure of human IL-1beta in complex with a low molecular weight antagonist
ComponentsInterleukin-1 beta
KeywordsCYTOKINE / Beta Trefoil fold / secreted
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 D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / positive regulation of cell adhesion molecule production ...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 D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / positive regulation of cell adhesion molecule production / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / sequestering of triglyceride / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of prostaglandin secretion / positive regulation of neuroinflammatory response / 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 / response to carbohydrate / positive regulation of monocyte chemotactic protein-1 production / interleukin-1 receptor binding / 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 / Interleukin-10 signaling / 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 / negative regulation of MAP kinase activity / positive regulation of T cell proliferation / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / JNK cascade / negative regulation of insulin receptor signaling pathway / neutrophil chemotaxis / embryo implantation / positive regulation of interleukin-2 production / regulation of insulin secretion / positive regulation of mitotic nuclear division / response to interleukin-1 / regulation of ERK1 and ERK2 cascade / positive regulation of protein export from nucleus / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of DNA-binding transcription factor activity / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / negative regulation of neurogenesis / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / 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 / immune response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / protein domain specific binding / positive regulation of cell population proliferation / positive regulation of gene expression
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
Similarity search - Domain/homology
Chem-T9C / Interleukin-1 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 Å
AuthorsRondeau, J.-M. / Lehmann, S. / Koch, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Discovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1 beta.
Authors: Hommel, U. / Hurth, K. / Rondeau, J.M. / Vulpetti, A. / Ostermeier, D. / Boettcher, A. / Brady, J.P. / Hediger, M. / Lehmann, S. / Koch, E. / Blechschmidt, A. / Yamamoto, R. / Tundo ...Authors: Hommel, U. / Hurth, K. / Rondeau, J.M. / Vulpetti, A. / Ostermeier, D. / Boettcher, A. / Brady, J.P. / Hediger, M. / Lehmann, S. / Koch, E. / Blechschmidt, A. / Yamamoto, R. / Tundo Dottorello, V. / Haenni-Holzinger, S. / Kaiser, C. / Lehr, P. / Lingel, A. / Mureddu, L. / Schleberger, C. / Blank, J. / Ramage, P. / Freuler, F. / Eder, J. / Bornancin, F.
History
DepositionDec 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 beta
B: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7314
Polymers34,7922
Non-polymers9392
Water3,639202
1
A: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8652
Polymers17,3961
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8652
Polymers17,3961
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.168, 60.085, 55.877
Angle α, β, γ (deg.)90.00, 114.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interleukin-1 beta / IL-1 beta / Catabolin


Mass: 17395.832 Da / Num. of mol.: 2 / Fragment: Fab light-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL23 (DE3) / References: UniProt: P01584
#2: Chemical ChemComp-T9C / (S)-4'-hydroxy-3'-(6-methyl-2-oxo-3-(1H-pyrazol-4-yl)indolin-3-yl)-[1,1'-biphenyl]-2,4-dicarboxylic acid / 4-[3-[(3S)-6-methyl-2-oxidanylidene-3-(1H-pyrazol-4-yl)-1H-indol-3-yl]-4-oxidanyl-phenyl]benzene-1,3-dicarboxylic acid


Mass: 469.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H19N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.01M sodium citrate, 33% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000036 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000036 Å / Relative weight: 1
ReflectionResolution: 1.945→50.741 Å / Num. obs: 24314 / % possible obs: 97.4 % / Redundancy: 5.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.058 / Rrim(I) all: 0.131 / Net I/σ(I): 7.6
Reflection shellResolution: 1.945→1.978 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.039 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1178 / CC1/2: 0.326 / Rpim(I) all: 0.959 / Rrim(I) all: 2.256 / % possible all: 97

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Processing

Software
NameClassification
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I1B

2i1b


Resolution: 1.945→50.74 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1185 4.89 %RANDOM
Rwork0.2077 ---
obs0.2093 24237 97.1 %-
Displacement parametersBiso mean: 44.04 Å2
Baniso -1Baniso -2Baniso -3
1--4.3712 Å20 Å20.5736 Å2
2---1.2949 Å20 Å2
3---5.6662 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.945→50.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 70 202 2696
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082548HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.113442HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d908SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes430HARMONIC5
X-RAY DIFFRACTIONt_it2548HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.18
X-RAY DIFFRACTIONt_other_torsion15.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion312SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2015SEMIHARMONIC4
LS refinement shellResolution: 1.95→1.96 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2574 -4.33 %
Rwork0.3165 464 -
all0.314 485 -
obs--92.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.81430.5604-0.27362.12470.99772.79340.0623-0.3626-0.0758-0.1675-0.1844-0.0252-0.10970.03960.1221-0.058-0.0048-0.00880.03620.0297-0.1303-15.8303-8.3104-55.8763
24.1834-0.46780.81311.0599-0.0561.4432-0.04260.2346-0.13930.05410.05620.02890.08170.0782-0.0135-0.01130.0008-0.0043-0.0674-0.0067-0.0427-8.3895-12.5483-24.7253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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