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- PDB-9od7: Structure of disulfide-stabilized IL-18 variant -

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Basic information

Entry
Database: PDB / ID: 9od7
TitleStructure of disulfide-stabilized IL-18 variant
ComponentsInterleukin-18
KeywordsCYTOKINE / protein structure
Function / homology
Function and homology information


interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / positive regulation of neuroinflammatory response / neutrophil activation / negative regulation of myoblast differentiation ...interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / positive regulation of neuroinflammatory response / neutrophil activation / negative regulation of myoblast differentiation / Interleukin-1 processing / sleep / positive regulation of NK T cell proliferation / positive regulation of macrophage derived foam cell differentiation / natural killer cell activation / positive regulation of granulocyte macrophage colony-stimulating factor production / type 2 immune response / triglyceride homeostasis / positive regulation of tyrosine phosphorylation of STAT protein / T-helper 1 type immune response / natural killer cell mediated cytotoxicity / Interleukin-10 signaling / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / positive regulation of natural killer cell proliferation / Pyroptosis / establishment of skin barrier / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cholesterol homeostasis / cytokine activity / positive regulation of smooth muscle cell proliferation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / cytokine-mediated signaling pathway / positive regulation of type II interferon production / positive regulation of inflammatory response / cell-cell signaling / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / immune response / inflammatory response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol
Similarity search - Function
Interleukin-18 / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSun, D. / Masureel, M. / Bainbridge, T. / Bulutoglu, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Immunother Cancer / Year: 2025
Title: Engineered IL-18 variants with half-life extension and improved stability for cancer immunotherapy.
Authors: Bainbridge, T.W. / Wang, L. / Moskalenko, M. / Herrera, R. / Paluch, M.T. / Sun, D. / Tasneem, K. / Saini, H. / Sadek, M. / Kwong, M. / Kim, Y.M. / Bhatt, J.M. / Tam, C. / Chan, P.P.F. / ...Authors: Bainbridge, T.W. / Wang, L. / Moskalenko, M. / Herrera, R. / Paluch, M.T. / Sun, D. / Tasneem, K. / Saini, H. / Sadek, M. / Kwong, M. / Kim, Y.M. / Bhatt, J.M. / Tam, C. / Chan, P.P.F. / Ovacik, A.M. / Masureel, M. / Zhao, Y. / Sockolosky, J.T. / Qu, Y. / West, N.R. / Bulutoglu, B.
History
DepositionApr 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-18


Theoretical massNumber of molelcules
Total (without water)19,1051
Polymers19,1051
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.916, 70.916, 89.904
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Interleukin-18 / IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 ...IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 gamma / IL-1 gamma


Mass: 19105.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18, IGIF, IL1F4 / Production host: Homo sapiens (human) / References: UniProt: Q14116
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 273.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M MIB buffer (mixing sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3), pH 4.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.895→50.712 Å / Num. obs: 18169 / % possible obs: 89.1 % / Redundancy: 9.7 % / CC1/2: 1 / Net I/σ(I): 24.3
Reflection shellResolution: 1.895→1.928 Å / Num. unique obs: 1017 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.27 Å / SU ML: 0.1831 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1954 888 4.92 %
Rwork0.1575 17147 -
obs0.1593 18035 89.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 0 121 1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691294
X-RAY DIFFRACTIONf_angle_d0.96471734
X-RAY DIFFRACTIONf_chiral_restr0.0615187
X-RAY DIFFRACTIONf_plane_restr0.008228
X-RAY DIFFRACTIONf_dihedral_angle_d6.4817169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.20681660.19273218X-RAY DIFFRACTION99.94
2.02-2.170.2327850.15642232X-RAY DIFFRACTION69.33
2.18-2.390.21331660.18922835X-RAY DIFFRACTION89.37
2.39-2.740.22281350.17622566X-RAY DIFFRACTION79.98
2.74-3.450.19821710.16623195X-RAY DIFFRACTION99.97
3.45-36.270.17751650.13553101X-RAY DIFFRACTION95.47
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)
11.0007918320.221766458102-0.1484889144520.663388191324-1.314115399790.8273933434960.0137143296843-0.07528443819580.06491649957570.1035226228710.07246333461360.04482571183320.0261948808161-0.0713485705595-2.67583895937E-50.2080774892870.0111803828645-0.005375924304040.215549960708-0.008847575537620.225527092419-7.37688051257-34.13051391093.48821198227
21.19556449913-0.1766824926820.1968700176421.41980600898-0.1138771118912.62442754878-0.03090715289720.06588515624610.03472289646370.07003742692870.01213983321840.0132551880404-0.132572259346-0.112039991093-1.33272056132E-60.2080659993020.0103860202056-0.02111037377470.1889774275770.008717118277680.213793929454-4.27237939376-29.6986425151-7.75735926375
30.895980770851-0.5283006898660.5076832186531.06561770352-0.4101270662561.48279626351-0.0104506590908-0.05061911746710.1782462029920.199683667436-0.102825933458-0.0381868613648-0.138383794580.113035529615-0.0008115454930230.252362528385-0.0397666974228-0.0250664145290.201533382267-0.001035420184310.2583148509652.5735712621-26.99631056162.48817424081
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 90 )37 - 901 - 54
22chain 'A' and (resid 91 through 153 )91 - 15355 - 117
33chain 'A' and (resid 154 through 194 )154 - 194118 - 158

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