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- PDB-3f62: Crystal Structure of Human IL-18 in complex with Ectromelia virus... -

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Basic information

Entry
Database: PDB / ID: 3f62
TitleCrystal Structure of Human IL-18 in complex with Ectromelia virus IL-18 Binding Protein
Components
  • Interleukin 18 binding protein
  • Interleukin-18Interleukin 18
KeywordsCYTOKINE / immunoglobulin / IL-18 / beta trefoil / Secreted
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 / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity ...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 / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity / triglyceride homeostasis / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / sleep / Interleukin-1 processing / positive regulation of NK T cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of interleukin-13 production / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / positive regulation of natural killer cell proliferation / establishment of skin barrier / Pyroptosis / Purinergic signaling in leishmaniasis infection / regulation of cell adhesion / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / 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 NF-kappaB transcription factor activity / positive regulation of cold-induced thermogenesis / 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 / inflammatory response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol
Similarity search - Function
Orthopoxvirus interleukin 18 binding / Orthopoxvirus interleukin 18 binding protein / 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 / Immunoglobulins ...Orthopoxvirus interleukin 18 binding / Orthopoxvirus interleukin 18 binding protein / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-18 / EVM013 / Interleukin 18 binding protein
Similarity search - Component
Biological speciesEctromelia virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKrumm, B.E. / Li, Y. / Deng, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural basis for antagonism of human interleukin 18 by poxvirus interleukin 18-binding protein.
Authors: Krumm, B. / Meng, X. / Li, Y. / Xiang, Y. / Deng, J.
History
DepositionNov 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin 18 binding protein
B: Interleukin-18


Theoretical massNumber of molelcules
Total (without water)30,6012
Polymers30,6012
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-13 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.356, 69.210, 104.832
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: Antibody Interleukin 18 binding protein


Mass: 12368.020 Da / Num. of mol.: 1 / Fragment: UNP residues 21-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectromelia virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9IW12, UniProt: Q85319*PLUS
#2: Protein Interleukin-18 / Interleukin 18 / IL-18 / Interferon-gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 gamma / IL-1 ...IL-18 / Interferon-gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 gamma / IL-1 gamma / Iboctadekin


Mass: 18232.518 Da / Num. of mol.: 1 / Fragment: UNP residues 37-193 / Mutation: C38S, C68S, C76S, C127S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18, IGIF, IL1F4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14116
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 30% Peg 3350, 0.5M KCl, 0.1M Sodium Citrate, pH 4.5, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Apr 3, 2004
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 18358 / Num. obs: 17333 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rsym value: 0.094 / Net I/σ(I): 12.66
Reflection shellResolution: 2→2.048 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.568 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
RefinementResolution: 2→34.61 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0 / SU B: 7.26 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23545 940 5.1 %RANDOM
Rwork0.18856 ---
obs0.19089 17333 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.563 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 120 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221957
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9442636
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20624.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.655158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021444
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2747
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21332
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8591.51280
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31621997
X-RAY DIFFRACTIONr_scbond_it2.1933769
X-RAY DIFFRACTIONr_scangle_it3.3044.5639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 67 -
Rwork0.205 1016 -
obs--79.69 %
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)
13.4928-3.72380.39825.884-0.76721.14220.23420.38920.0883-0.2753-0.2864-0.13730.03290.05570.05220.0865-0.00210.00870.0585-0.00190.012714.842312.1492-8.4164
21.437-1.4729-0.01964.08330.51342.3704-0.0133-0.0825-0.10550.15420.00420.10640.3073-0.06780.0090.0623-0.0170.00270.0539-0.00640.059716.17991.10493.1811
31.9553-0.5042-0.46134.0350.47713.13280.02150.03250.0147-0.0799-0.0621-0.020.05520.02770.04050.0468-0.0126-0.00080.060.00590.068221.456610.57490.5766
42.4664-3.0481-1.73934.87012.27983.02750.06950.1776-0.1489-0.1456-0.08720.12360.1901-0.13650.01770.0885-0.0223-0.00650.0258-0.02570.076714.618-1.7985-2.6749
51.6966-0.6133-1.31361.88611.34283.45040.0561-0.2220.10130.05570.0061-0.0068-0.21110.0505-0.06220.05360.011-0.01610.05990.02990.01238.731513.367227.5442
61.87290.5425-0.29996.15624.43947.2594-0.0171-0.1394-0.0070.1795-0.0351-0.00150.17150.07560.05220.02-0.00160.02930.06570.03530.055711.39215.546218.226
72.5565-0.86120.0872.4570.64162.5651-0.1021-0.142-0.24620.12840.04630.05130.37940.00070.05570.0654-0.00460.02320.03750.04730.04457.44971.440123.0638
82.9815-0.0233-0.64612.6565-0.41392.4903-0.0134-0.17430.0080.01550.10630.199-0.1415-0.1973-0.09290.0121-0.0017-0.00510.0760.03110.0261-2.25912.813820.3299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 18
2X-RAY DIFFRACTION2A19 - 57
3X-RAY DIFFRACTION3A58 - 79
4X-RAY DIFFRACTION4A80 - 106
5X-RAY DIFFRACTION5B0 - 46
6X-RAY DIFFRACTION6B47 - 70
7X-RAY DIFFRACTION7B71 - 104
8X-RAY DIFFRACTION8B105 - 155

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