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- PDB-4g6m: Crystal structure of human IL-1beta in complex with therapeutic a... -

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Basic information

Entry
Database: PDB / ID: 4g6m
TitleCrystal structure of human IL-1beta in complex with therapeutic antibody binding fragment of gevokizumab
Components
  • Interleukin-1 beta
  • heavy chain of gevokizumab antibody binding fragment
  • light chain of gevokizumab antibody binding fragment
KeywordsIMMUNE SYSTEM / immunoglobulin fold / interleukine-1beta
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 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 / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / Interleukin-1 processing / response to carbohydrate / negative regulation of synaptic transmission / 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 / 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 / positive regulation of vascular endothelial growth factor production / regulation of neurogenesis / ectopic germ cell programmed cell death / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of glial cell proliferation / positive regulation of T cell proliferation / neutrophil chemotaxis / embryo implantation / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / regulation of insulin secretion / response to interleukin-1 / negative regulation of insulin receptor signaling pathway / 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 / cellular response to mechanical stimulus / Interleukin-1 signaling / positive regulation of type II interferon production / positive regulation of inflammatory response / positive regulation of angiogenesis / 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 / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / 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 / apoptotic process / 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 / 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)
homo Sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsBlech, M. / Hoerer, S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal structure of human IL-1beta in complex with therapeutic antibody binding fragment of gevokizumab
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 1.2Feb 5, 2014Group: Other
Revision 1.3Mar 12, 2014Group: Other
Revision 1.4Dec 14, 2016Group: Structure summary
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_sheet.number_strands
Revision 1.6Oct 30, 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 gevokizumab antibody binding fragment
L: light chain of gevokizumab antibody binding fragment


Theoretical massNumber of molelcules
Total (without water)64,0713
Polymers64,0713
Non-polymers00
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.884, 73.651, 111.254
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: 17150.596 Da / Num. of mol.: 1 / Fragment: unp residues 117-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01584
#2: Antibody heavy chain of gevokizumab antibody binding fragment


Mass: 23420.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo Sapiens, Mus musculus / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody light chain of gevokizumab antibody binding fragment


Mass: 23500.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo Sapiens, Mus musculus / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 293 K / pH: 5
Details: 20% w/v PEG 4000, 0.2M ammonium formate supplemented with 10% w/v polyvinylpyrrolidone K15, pH 5.0, 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
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→111.3 Å / Num. obs: 51619 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 25.54 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.093 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 14.6 / % possible all: 100

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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: 1.81→26.5 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2589 5.08 %RANDOM
Rwork0.202 ---
obs0.203 50918 98.8 %-
all-51619 --
Displacement parametersBiso mean: 31.09 Å2
Baniso -1Baniso -2Baniso -3
1--4.713 Å20 Å20 Å2
2--1.5524 Å20 Å2
3---3.1607 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.81→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 0 442 4943
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074610HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.026258HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1567SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2
X-RAY DIFFRACTIONt_gen_planes656HARMONIC5
X-RAY DIFFRACTIONt_it4610HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion17.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion605SEMIHARMONIC5
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_contact5276SEMIHARMONIC4
LS refinement shellResolution: 1.81→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2371 195 5.19 %
Rwork0.2094 3562 -
all0.2108 3757 -
obs--98.77 %
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)
11.49280.2019-0.01231.4742-0.51523.2018-0.03130.23380.0888-0.26080.0157-0.07360.07580.10790.0156-0.0272-0.03810.0287-0.04830.0262-0.09254.117929.9202-25.9963
20.1055-0.0092-0.1780.4571-0.44971.47030.00520.02450.0058-0.04020.03430.05780.1514-0.0486-0.0395-0.0341-0.01350.002-0.0387-0.0035-0.01815.154919.811318.908
30.2419-0.1182-0.38530.40350.32942.0441-0.02920.00520.03320.06760.02-0.00110.0068-0.15960.0092-0.0423-0.0008-0.0131-0.0542-0.0005-0.0361-3.825734.670724.0628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|151 }
2X-RAY DIFFRACTION2{ H|1 - H|220 }
3X-RAY DIFFRACTION3{ L|1 - L|213 }

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