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- PDB-4g6j: Crystal structure of human IL-1beta in complex with the therapeut... -

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Basic information

Entry
Database: PDB / ID: 4g6j
TitleCrystal structure of human IL-1beta in complex with the therapeutic antibody binding fragment of canakinumab
Components
  • Interleukin-1 beta
  • heavy chain of antibody binding fragment of canakinumab
  • light chain of antibody binding fragment of canakinumab
KeywordsIMMUNE SYSTEM / immunglobulin fold / interleukin-1beta binding
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 prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of neuroinflammatory response / regulation of defense response to virus by host / positive regulation of platelet-derived growth factor receptor signaling pathway / fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of monocyte chemotactic protein-1 production / positive regulation of p38MAPK cascade / positive regulation of macrophage derived foam cell differentiation / negative regulation of synaptic transmission / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of vascular endothelial growth factor production / positive regulation of cell division / positive regulation of glial cell proliferation / Pyroptosis / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / positive regulation of epithelial to mesenchymal transition / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / negative regulation of MAPK cascade / JNK cascade / positive regulation of T cell proliferation / neutrophil chemotaxis / extrinsic apoptotic signaling pathway in absence of ligand / embryo implantation / positive regulation of interleukin-2 production / astrocyte activation / regulation of insulin secretion / positive regulation of mitotic nuclear division / negative regulation of insulin receptor signaling pathway / response to interleukin-1 / secretory granule / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of neurogenesis / positive regulation of interleukin-6 production / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / integrin binding / Interleukin-1 signaling / cytokine-mediated signaling pathway / positive regulation of angiogenesis / positive regulation of inflammatory response / positive regulation of nitric oxide biosynthetic process / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / positive regulation of cell population proliferation / apoptotic process / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBlech, M. / Hoerer, S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: One traget-two different binding modes: Structural insights into gevokizumab and canakinumab interactions to interleukin-1beta
Authors: Blech, M. / Peter, D. / Fischer, P. / Bauer, M.M. / Hafner, M. / Zeeb, M. / Nar, H.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 beta
H: heavy chain of antibody binding fragment of canakinumab
L: light chain of antibody binding fragment of canakinumab


Theoretical massNumber of molelcules
Total (without water)64,4923
Polymers64,4923
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.061, 37.300, 189.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17993.629 Da / Num. of mol.: 1 / Fragment: human interleukin-1beta / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01584
#2: Antibody heavy chain of antibody binding fragment of canakinumab


Mass: 23349.152 Da / Num. of mol.: 1
Fragment: heavy chain of antibody binding fragment of canakinumab
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Antibody light chain of antibody binding fragment of canakinumab


Mass: 23149.652 Da / Num. of mol.: 1
Fragment: light chain of antibody binding fragment of canakinumab
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 17.2% w/v PEG 3350 and 0.14M tri-sodium citrate, 24% w/v PEG 3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→94.7 Å / Num. all: 207933 / Num. obs: 38275 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 29.23 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.12 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 2.3 / Num. unique all: 37806 / Rsym value: 0.12 / % possible all: 93.5

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Processing

Software
NameVersionClassification
XDSdata scaling
autoPROCdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
autoPROCdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ5, 3BKJ, 1TOO

1pz5

3bkj

1too


Resolution: 2.03→39.36 Å / Cor.coef. Fo:Fc: 0.9065 / Cor.coef. Fo:Fc free: 0.8926 / SU R Cruickshank DPI: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1891 5.02 %RANDOM
Rwork0.2257 ---
obs0.227 37684 98.59 %-
all-37806 --
Displacement parametersBiso mean: 35.92 Å2
Baniso -1Baniso -2Baniso -3
1--7.0896 Å20 Å20 Å2
2---0.8482 Å20 Å2
3---7.9378 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.03→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 0 303 4769
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074575HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.026211HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1550SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes657HARMONIC5
X-RAY DIFFRACTIONt_it4575HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion17.04
X-RAY DIFFRACTIONt_chiral_improper_torsion595SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5151SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.09 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.22 143 5.2 %
Rwork0.2173 2606 -
all0.2175 2749 -
obs--98.59 %
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)
12.05830.884-0.45221.5259-0.76331.69680.0075-0.13590.01770.2270.07060.0632-0.0396-0.3307-0.07810.0451-0.03110.02250.01390.0324-0.171118.5512-12.2017-36.2569
20.16880.1613-0.3350.5104-0.00732.43570.0509-0.0232-0.0058-0.03060.0455-0.0485-0.0070.1515-0.0965-0.02350.0175-0.0106-0.098-0.0125-0.049537.6745-8.8056-76.0438
30.7887-0.1068-0.13990.2833-0.27712.13850.04230.05-0.0655-0.10210.0240.044-0.0665-0.2651-0.0663-0.01780.0025-0.0193-0.1218-0.0026-0.08221.9125-5.665-84.925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|4 - A|152 }A4 - 152
2X-RAY DIFFRACTION2{ H|1 - H|218 }H1 - 218
3X-RAY DIFFRACTION3{ L|1 - L|212 }L1 - 212

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