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

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Basic information

Entry
Database: PDB / ID: 7chz
TitleCrystal Structure Of Human Il-1beta In Complex With Antibody Binding Fragment Of IgG26A
Components
  • Interleukin-1 beta
  • heavy chain of antibody binding fragment of IgG26A
  • light chain of antibody binding fragment of IgG26A
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 / negative regulation of glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...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 glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / 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 / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / neutrophil activation / 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 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 / : / 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 / positive regulation of glial cell proliferation / JNK cascade / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / embryo implantation / 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 / positive regulation of interleukin-8 production / astrocyte activation / 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 / Interleukin-1 signaling / positive regulation of inflammatory response / 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 / 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 / positive regulation of protein phosphorylation / immune response / negative regulation of cell population proliferation
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: 2.5 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 IgG26A
H: heavy chain of antibody binding fragment of IgG26A
I: Interleukin-1 beta


Theoretical massNumber of molelcules
Total (without water)65,5963
Polymers65,5963
Non-polymers00
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-33 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.694, 112.699, 38.935
Angle α, β, γ (deg.)90.000, 94.531, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody light chain of antibody binding fragment of IgG26A


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 IgG26A


Mass: 24397.430 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 / 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


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 17% (w/v) PEG 3350, 10% (v/v) glycerol, and 0.1 M citric acid at pH 4.0

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.48→25 Å / Num. obs: 23536 / % possible obs: 98.9 % / Redundancy: 3.7 % / CC1/2: 0.88 / CC star: 0.97 / Net I/σ(I): 28.8
Reflection shellResolution: 2.48→2.57 Å / Num. unique obs: 2268 / CC1/2: 0.88 / CC star: 0.97

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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: 2.5→23.941 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.888 / SU B: 18.503 / SU ML: 0.227 / Cross valid method: FREE R-VALUE / ESU R: 0.658 / ESU R Free: 0.31
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2595 1142 4.967 %
Rwork0.1926 21849 -
all0.196 --
obs-22991 98.916 %
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: 52.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.111 Å2-0 Å20.384 Å2
2--0.164 Å20 Å2
3----0.332 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4465 0 0 329 4794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134572
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174119
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6436206
X-RAY DIFFRACTIONr_angle_other_deg1.2151.5729626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.145574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5723.689206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18715760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7191516
X-RAY DIFFRACTIONr_chiral_restr0.0660.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
X-RAY DIFFRACTIONr_nbd_refined0.180.2685
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23753
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22051
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22075
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.235
X-RAY DIFFRACTIONr_nbd_other0.220.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.213
X-RAY DIFFRACTIONr_mcbond_it2.2233.1552308
X-RAY DIFFRACTIONr_mcbond_other2.2213.1532307
X-RAY DIFFRACTIONr_mcangle_it3.9584.7112878
X-RAY DIFFRACTIONr_mcangle_other3.9574.7122879
X-RAY DIFFRACTIONr_scbond_it1.6433.2912264
X-RAY DIFFRACTIONr_scbond_other1.6413.2912264
X-RAY DIFFRACTIONr_scangle_it3.0064.8243328
X-RAY DIFFRACTIONr_scangle_other3.0064.8253329
X-RAY DIFFRACTIONr_lrange_it6.8133.8984704
X-RAY DIFFRACTIONr_lrange_other6.75933.8294676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5640.371830.2511573X-RAY DIFFRACTION97.5265
2.564-2.6340.344680.2421581X-RAY DIFFRACTION99.6977
2.634-2.7090.35800.2421521X-RAY DIFFRACTION99.5028
2.709-2.7920.309810.2421487X-RAY DIFFRACTION99.3663
2.792-2.8820.368680.2361416X-RAY DIFFRACTION99.8654
2.882-2.9820.287970.2021392X-RAY DIFFRACTION99.2005
2.982-3.0930.276970.2161283X-RAY DIFFRACTION99.8553
3.093-3.2170.237630.2171310X-RAY DIFFRACTION99.2052
3.217-3.3570.273590.2091218X-RAY DIFFRACTION99.61
3.357-3.5180.287750.1941201X-RAY DIFFRACTION99.0683
3.518-3.7040.215600.1861106X-RAY DIFFRACTION99.6581
3.704-3.9240.254600.1831075X-RAY DIFFRACTION98.9538
3.924-4.1870.212400.1731003X-RAY DIFFRACTION99.5229
4.187-4.5120.192370.161944X-RAY DIFFRACTION99.1911
4.512-4.9270.224440.156887X-RAY DIFFRACTION99.3597
4.927-5.4820.204240.151806X-RAY DIFFRACTION99.6399
5.482-6.2790.212460.166700X-RAY DIFFRACTION99.7326
6.279-7.5720.235220.178609X-RAY DIFFRACTION99.0581
7.572-10.2490.21240.16471X-RAY DIFFRACTION97.8261
10.249-230.266130.195260X-RAY DIFFRACTION82.7273
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)
11.78861.82540.30581.88410.32760.07420.0217-0.07430.52730.0547-0.12290.60130.066-0.06770.10120.1919-0.1481-0.02710.1456-0.08910.455647.2487-15.609-0.6976
20.0561-0.014-0.13440.84310.69220.8538-0.02470.09220.05610.06140.08510.05280.0553-0.1548-0.06040.1956-0.0284-0.0380.25790.01250.147165.2167-9.62760.089
32.4367-2.05990.16294.2450.55210.2042-0.643-0.20510.0340.53310.6310.0631-0.03670.11670.0120.36570.19840.01910.21230.04750.072654.856628.952725.4039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLL1 - 212
2X-RAY DIFFRACTION2ALLH1 - 220
3X-RAY DIFFRACTION3ALLI119 - 269

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