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- PDB-7chy: Crystal Structure Of Human Il-1beta In Complex With Antibody Bind... -

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Basic information

Entry
Database: PDB / ID: 7chy
TitleCrystal Structure Of Human Il-1beta In Complex With Antibody Binding Fragment Of IgG26
Components
  • Interleukin-1 betaInterleukin 1 beta
  • heavy chain of antibody binding fragment of IgG26
  • light chain of antibody binding fragment of IgG26
KeywordsIMMUNOSUPPRESSANT / complex / antibody / interleukin-1beta
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 / hyaluronan biosynthetic process / negative regulation of glucose transmembrane transport / 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 / hyaluronan biosynthetic process / negative regulation of glucose transmembrane transport / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / cellular response to interleukin-17 / sequestering of triglyceride / positive regulation of RNA biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / neutrophil activation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of monocyte chemotactic protein-1 production / 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 granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / positive regulation of membrane protein ectodomain proteolysis / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / : / regulation of nitric-oxide synthase activity / response to ATP / macrophage chemotaxis / Interleukin-10 signaling / regulation of insulin secretion / 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 / positive regulation of T cell proliferation / JNK cascade / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / embryo implantation / negative regulation of insulin receptor signaling pathway / response to interleukin-1 / positive regulation of mitotic nuclear division / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / positive regulation of protein export from nucleus / negative regulation of MAP kinase activity / secretory granule / cytokine activity / astrocyte activation / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis / positive regulation of inflammatory response / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of angiogenesis / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / integrin binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / response to lipopolysaccharide / lysosome / positive regulation of cell migration / defense response to Gram-positive bacterium / inflammatory response / immune response / positive regulation of protein phosphorylation / protein domain specific binding
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 / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLee, C.C. / Wang, A.H.J. / Kuo, W.C.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structure-based Development of Human Interleukin-1 beta-Specific Antibody That Simultaneously Inhibits Binding to Both IL-1RI and IL-1RAcP.
Authors: Kuo, W.C. / Lee, C.C. / Chang, Y.W. / Pang, W. / Chen, H.S. / Hou, S.C. / Lo, S.Y. / Yang, A.S. / Wang, A.H.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: light chain of antibody binding fragment of IgG26
H: heavy chain of antibody binding fragment of IgG26
I: Interleukin-1 beta


Theoretical massNumber of molelcules
Total (without water)66,4843
Polymers66,4843
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-33 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.344, 112.240, 38.577
Angle α, β, γ (deg.)90.000, 94.847, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody light chain of antibody binding fragment of IgG26


Mass: 23387.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody heavy chain of antibody binding fragment of IgG26


Mass: 25285.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Interleukin-1 beta / Interleukin 1 beta / IL-1 beta / Catabolin


Mass: 17810.316 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 17% (w/v) PEG 3350, 10% (v/v) glycerol, and 0.1 M citric acid at pH 3.8.

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→19.763 Å / Num. obs: 19167 / % possible obs: 100 % / Redundancy: 2.7 % / CC1/2: 0.76 / CC star: 0.93 / Net I/σ(I): 20.7
Reflection shellResolution: 2.65→2.74 Å / Num. unique obs: 1911 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I1B

2i1b


Resolution: 2.65→19.7 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 24.739 / SU ML: 0.285 / Cross valid method: FREE R-VALUE / ESU R Free: 0.366
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2535 963 5.32 %
Rwork0.1998 17140 -
all0.203 --
obs-18103 93.696 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 64.403 Å2
Baniso -1Baniso -2Baniso -3
1-2.417 Å2-0 Å20.882 Å2
2---2.815 Å2-0 Å2
3---0.245 Å2
Refinement stepCycle: LAST / Resolution: 2.65→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4428 0 0 280 4708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134536
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174069
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.6426160
X-RAY DIFFRACTIONr_angle_other_deg1.1061.5729509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82123.725204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43815747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3491515
X-RAY DIFFRACTIONr_chiral_restr0.0420.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02919
X-RAY DIFFRACTIONr_nbd_refined0.1650.2692
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.23803
X-RAY DIFFRACTIONr_nbtor_refined0.1560.22086
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0660.22048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1240.222
X-RAY DIFFRACTIONr_nbd_other0.1790.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.210
X-RAY DIFFRACTIONr_mcbond_it1.4023.1912288
X-RAY DIFFRACTIONr_mcbond_other1.4023.1892287
X-RAY DIFFRACTIONr_mcangle_it2.6064.7752853
X-RAY DIFFRACTIONr_mcangle_other2.6064.7772854
X-RAY DIFFRACTIONr_scbond_it0.7443.2712248
X-RAY DIFFRACTIONr_scbond_other0.7443.2712248
X-RAY DIFFRACTIONr_scangle_it1.5414.8343307
X-RAY DIFFRACTIONr_scangle_other1.544.8353308
X-RAY DIFFRACTIONr_lrange_it5.70134.1924733
X-RAY DIFFRACTIONr_lrange_other5.59434.0464702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.7180.341500.264847X-RAY DIFFRACTION64.8121
2.718-2.7910.288530.27955X-RAY DIFFRACTION73.6842
2.791-2.870.372620.2651025X-RAY DIFFRACTION83.4869
2.87-2.9560.348800.2571209X-RAY DIFFRACTION97.5776
2.956-3.0510.288860.2481152X-RAY DIFFRACTION100
3.051-3.1550.287690.2261140X-RAY DIFFRACTION100
3.155-3.2710.254580.2191103X-RAY DIFFRACTION99.828
3.271-3.4010.292640.2171074X-RAY DIFFRACTION99.5626
3.401-3.5480.277690.2041017X-RAY DIFFRACTION99.5417
3.548-3.7150.226570.2957X-RAY DIFFRACTION99.9015
3.715-3.9090.267340.206969X-RAY DIFFRACTION99.7018
3.909-4.1360.259470.191880X-RAY DIFFRACTION99.4635
4.136-4.4080.174390.164853X-RAY DIFFRACTION99.7763
4.408-4.7420.172380.151787X-RAY DIFFRACTION99.5175
4.742-5.1660.163490.153700X-RAY DIFFRACTION99.4688
5.166-5.7280.323340.179669X-RAY DIFFRACTION99.5751
5.728-6.5250.231170.196614X-RAY DIFFRACTION99.5268
6.525-7.7870.302220.188513X-RAY DIFFRACTION99.2579
7.787-10.2630.2220.169397X-RAY DIFFRACTION97.669
10.263-19.7630.196130.186278X-RAY DIFFRACTION94.4805
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)
10.58561.3640.16554.22111.3250.92150.01310.32190.15880.303-0.02870.22050.2469-0.66340.01550.0725-0.1918-0.04740.85520.00940.435847.6062-15.6055-0.7125
20.41480.322-0.23681.41591.23262.0293-0.08710.21420.12780.13940.21150.08190.2446-0.3014-0.12440.2061-0.0551-0.08330.56780.04490.228565.5399-9.89460.1532
31.1529-1.01160.42344.59830.15151.0582-0.0308-0.0170.16570.64020.11660.3149-0.04660.0732-0.08580.36920.14130.18830.3524-0.02870.37954.851628.748425.2921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLL1 - 211
2X-RAY DIFFRACTION2ALLH3 - 220
3X-RAY DIFFRACTION3ALLI119 - 268

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