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- PDB-3wo2: Crystal structure of human interleukin-18 -

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Basic information

Entry
Database: PDB / ID: 3wo2
TitleCrystal structure of human interleukin-18
ComponentsInterleukin-18
KeywordsIMMUNE SYSTEM / beta trefoil fold / IL-1 superfamily / immunity / inflammation / autoimmunity / allergy / interleukin-18 receptor alpha / interleukin-18 receptor beta / serum
Function / homology
Function and homology information


interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / neutrophil activation / positive regulation of neuroinflammatory response / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway ...interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / neutrophil activation / positive regulation of neuroinflammatory response / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / Interleukin-1 processing / negative regulation of myoblast differentiation / type 2 immune response / sleep / natural killer cell activation / positive regulation of NK T cell proliferation / triglyceride homeostasis / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / natural killer cell mediated cytotoxicity / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / Pyroptosis / establishment of skin barrier / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of chemokine production / cholesterol homeostasis / cytokine activity / positive regulation of smooth muscle cell proliferation / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsTsutsumi, N. / Kimura, T. / Arita, K. / Ariyoshi, M. / Ohnishi, H. / Kondo, N. / Shirakawa, M. / Kato, Z. / Tochio, H.
CitationJournal: Nat Commun / Year: 2014
Title: The structural basis for receptor recognition of human interleukin-18
Authors: Tsutsumi, N. / Kimura, T. / Arita, K. / Ariyoshi, M. / Ohnishi, H. / Yamamoto, T. / Zuo, X. / Maenaka, K. / Park, E.Y. / Kondo, N. / Shirakawa, M. / Tochio, H. / Kato, Z.
History
DepositionDec 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Nov 8, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-18
B: Interleukin-18
C: Interleukin-18
D: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,72220
Polymers72,9594
Non-polymers7,76316
Water5,585310
1
A: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2766
Polymers18,2401
Non-polymers2,0375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1805
Polymers18,2401
Non-polymers1,9414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1805
Polymers18,2401
Non-polymers1,9414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0844
Polymers18,2401
Non-polymers1,8453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.146, 79.511, 73.460
Angle α, β, γ (deg.)90.00, 100.97, 90.00
Int Tables number4
Space group name H-MP1211

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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: 18239.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14116
#2: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-Tris-HCl, 2.5M ammonium sulfate, 0.2%(w/v) CHAPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→44.96 Å / Num. all: 33732 / Num. obs: 32990 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 50.14 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.5
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4746 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F62

3f62


Resolution: 2.33→34.82 Å / Cor.coef. Fo:Fc: 0.9228 / Cor.coef. Fo:Fc free: 0.8813 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.402 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.411 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.268 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 1638 5.09 %RANDOM
Rwork0.218 ---
obs0.2206 32157 97.3 %-
all-33049 --
Displacement parametersBiso max: 135.49 Å2 / Biso mean: 47.9386 Å2 / Biso min: 15.05 Å2
Baniso -1Baniso -2Baniso -3
1-5.8435 Å20 Å21.4184 Å2
2---2.3251 Å20 Å2
3----3.5184 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: LAST / Resolution: 2.33→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 401 310 5728
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2872SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes158HARMONIC2
X-RAY DIFFRACTIONt_gen_planes725HARMONIC5
X-RAY DIFFRACTIONt_it5540HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion815SEMIHARMONIC5
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_contact6437SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5540HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7546HARMONIC21.38
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion3.09
LS refinement shellResolution: 2.33→2.41 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2982 127 4.44 %
Rwork0.2759 2734 -
all0.277 2861 -
obs--97.3 %
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)
13.0957-0.6947-1.58762.30440.49715.43410.03420.15510.2044-0.13550.1316-0.34180.07580.388-0.1657-0.15620.00490.0126-0.1784-0.0822-0.0614-2.167495.9085115.1171
23.46061.1316-0.73342.6015-0.3683.98840.1217-0.5754-0.19550.221-0.12030.1297-0.0568-0.1268-0.0014-0.1606-0.00360.0275-0.08330.0837-0.135226.547593.267137.1816
32.59470.85970.61872.31551.08073.9480.0011-0.43820.15820.242-0.0856-0.04480.089-0.12670.0845-0.10550.00560.0285-0.1051-0.0703-0.1234-5.732568.0378106.8099
43.3687-0.09440.15121.3856-0.47925.92360.07240.580.1586-0.10.17970.1904-0.2718-0.2974-0.2521-0.1526-0.00230.0633-0.12760.1673-0.11320.136664.8837143.275
5-0.01580.1959-0.02080.0296-0.02280.6343-0.02720.11150.0718-0.0115-0.0061-0.02640.06620.06230.03330.0018-0.00240.0291-0.0852-0.0318-0.093911.458180.3071126.227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|157 }A1 - 157
2X-RAY DIFFRACTION2{ B|1 - B|156 }B1 - 156
3X-RAY DIFFRACTION3{ C|1 - C|157 }C1 - 157
4X-RAY DIFFRACTION4{ D|1 - D|157 }D1 - 157
5X-RAY DIFFRACTION5{ A|201 - A|203 B|201 - B|203 C|201 - C|203 D|201 - D|203}A201 - 203
6X-RAY DIFFRACTION5{ A|201 - A|203 B|201 - B|203 C|201 - C|203 D|201 - D|203}B201 - 203
7X-RAY DIFFRACTION5{ A|201 - A|203 B|201 - B|203 C|201 - C|203 D|201 - D|203}C201 - 203
8X-RAY DIFFRACTION5{ A|201 - A|203 B|201 - B|203 C|201 - C|203 D|201 - D|203}D201 - 203

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