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- PDB-8rys: Human IL-1beta, unliganded -

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Basic information

Entry
Database: PDB / ID: 8rys
TitleHuman IL-1beta, unliganded
ComponentsInterleukin-1 beta
KeywordsCYTOKINE / Interleukin
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.16 Å
AuthorsRondeau, J.-M. / Lehmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: J.Med.Chem. / Year: 2024
Title: Ligandability Assessment of IL-1 beta by Integrated Hit Identification Approaches.
Authors: Vulpetti, A. / Rondeau, J.M. / Bellance, M.H. / Blank, J. / Boesch, R. / Boettcher, A. / Bornancin, F. / Buhr, S. / Connor, L.E. / Dumelin, C.E. / Esser, O. / Hediger, M. / Hintermann, S. / ...Authors: Vulpetti, A. / Rondeau, J.M. / Bellance, M.H. / Blank, J. / Boesch, R. / Boettcher, A. / Bornancin, F. / Buhr, S. / Connor, L.E. / Dumelin, C.E. / Esser, O. / Hediger, M. / Hintermann, S. / Hommel, U. / Koch, E. / Lapointe, G. / Leder, L. / Lehmann, S. / Lehr, P. / Meier, P. / Muller, L. / Ostermeier, D. / Ramage, P. / Schiebel-Haddad, S. / Smith, A.B. / Stojanovic, A. / Velcicky, J. / Yamamoto, R. / Hurth, K.
#1: Journal: Nat Commun / Year: 2023
Title: Discovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1beta.
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
DepositionFeb 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4922
Polymers17,3961
Non-polymers961
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.784, 54.784, 76.173
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 17395.832 Da / Num. of mol.: 1 / Fragment: Fab light-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01584
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M TRIS pH 8.5, 2.4M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.16→44.476 Å / Num. obs: 71960 / % possible obs: 92.7 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.013 / Rrim(I) all: 0.033 / Net I/σ(I): 23.4
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2033 / CC1/2: 0.363 / Rpim(I) all: 0.762 / Rrim(I) all: 1.294 / % possible all: 52.8

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROC1.1.7data reduction
Aimless0.7.9data scaling
BUSTER2.11.8phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.16→27.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.035 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.037 / SU Rfree Blow DPI: 0.038 / SU Rfree Cruickshank DPI: 0.036
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 3620 5.03 %RANDOM
Rwork0.206 ---
obs0.2068 71921 92.7 %-
Displacement parametersBiso mean: 25.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.2732 Å20 Å20 Å2
2---0.2732 Å20 Å2
3---0.5465 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.16→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 5 168 1374
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0141237HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.341668HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d450SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes212HARMONIC5
X-RAY DIFFRACTIONt_it1237HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion156SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1159SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.22
X-RAY DIFFRACTIONt_other_torsion13.22
LS refinement shellResolution: 1.16→1.18 Å
RfactorNum. reflection% reflection
Rfree0.3056 77 -
Rwork0.3186 --
obs0.3178 1439 50.7 %
Refinement TLS params.Origin x: 11.5337 Å / Origin y: -14.1947 Å / Origin z: -1.5687 Å
111213212223313233
T-0.0198 Å20 Å20.0083 Å2--0.0147 Å20 Å2---0.0183 Å2
L0.6723 °20.0033 °20.3338 °2-1.3582 °20.3689 °2--0.9226 °2
S-0.0394 Å °0.0078 Å °0.025 Å °0.0078 Å °0.0457 Å °0.0013 Å °0.025 Å °0.0013 Å °-0.0064 Å °
Refinement TLS groupSelection details: { A|* }

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