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- PDB-2vxt: Crystal structure of human IL-18 complexed to murine reference an... -

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Basic information

Entry
Database: PDB / ID: 2vxt
TitleCrystal structure of human IL-18 complexed to murine reference antibody 125-2H Fab
Components
  • (MURINE IGG 125- ...) x 2
  • INTERLEUKIN-18
KeywordsCYTOKINE / FAB / IL-18 / SECRETED / AUTOIMMUNITY / GLYCOPROTEIN / TH1/TH2 CELLS / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN V REGION
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 / positive regulation of interleukin-13 production / 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 / positive regulation of interleukin-13 production / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / neutrophil activation / sleep / Interleukin-1 processing / 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 / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / establishment of skin barrier / Pyroptosis / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / cholesterol homeostasis / 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 / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsArgiriadi, M.A. / Xiang, T. / Wu, C. / Ghayur, T. / Borhani, D.W.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Unusual Water-Mediated Antigenic Recognition of the Proinflammatory Cytokine Interleukin-18.
Authors: Argiriadi, M.A. / Xiang, T. / Wu, C. / Ghayur, T. / Borhani, D.W.
History
DepositionJul 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: MURINE IGG 125-2H
I: INTERLEUKIN-18
L: MURINE IGG 125-2H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0936
Polymers64,9973
Non-polymers953
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-35.1 kcal/mol
Surface area31380 Å2
MethodPQS
Unit cell
Length a, b, c (Å)44.345, 62.435, 104.734
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules I

#2: Protein 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: 18111.467 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q14116

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Antibody , 2 types, 2 molecules HL

#1: Antibody MURINE IGG 125-2H


Mass: 23260.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#3: Antibody MURINE IGG 125-2H


Mass: 23625.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)

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Non-polymers , 3 types, 596 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN I, CYS 74 TO ALA ENGINEERED RESIDUE IN CHAIN I, CYS 104 TO ALA ...ENGINEERED RESIDUE IN CHAIN I, CYS 74 TO ALA ENGINEERED RESIDUE IN CHAIN I, CYS 104 TO ALA ENGINEERED RESIDUE IN CHAIN I, CYS 112 TO ALA ENGINEERED RESIDUE IN CHAIN I, CYS 163 TO ALA
Sequence detailsMATURE IL-18 COMPRISES RESIDUES 37-193. RESIDUES 1-36 OF PRO-IL-18 WERE NOT CRYSTALLIZED.

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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: 2.2 Å3/Da / Density % sol: 44.1 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: IL-18 AND 125-2H FAB WERE MIXED (1:3 MASS RATIO), INCUBATED OVERNIGHT AT 277 K, PURIFIED BY MONOQ ANION EXCHANGE CHROMATOGRAPHY, AND CONCENTRATED TO 10 MG/ML. THE COMPLEX WAS CRYSTALLIZED BY ...Details: IL-18 AND 125-2H FAB WERE MIXED (1:3 MASS RATIO), INCUBATED OVERNIGHT AT 277 K, PURIFIED BY MONOQ ANION EXCHANGE CHROMATOGRAPHY, AND CONCENTRATED TO 10 MG/ML. THE COMPLEX WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION BY MIXING COMPLEX (1.5 MICROLITERS [UL]) WITH 1.8 UL OF RESERVOIR SOLUTION (30% PEG 4000, 100 MM TRIS, PH 8.5, 0.2 M MGCL2) AND 0.3 UL OF 300 MM SULFO-BETAINE 201, AND SUSPENDING THE DROP OVER THE RESERVOIR AT 291 K. ROD-LIKE CRYSTALS APPEARED WITHIN ONE WEEK.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.00037
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 29, 2003 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00037 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 86865 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.3 / % possible all: 56.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FNS

1fns


Resolution: 1.49→31.16 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.971 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4364 5 %RANDOM
Rwork0.162 ---
obs0.164 82477 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20.84 Å2
2---0.33 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.49→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4485 0 3 593 5081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224921
X-RAY DIFFRACTIONr_bond_other_d0.0010.023323
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9556728
X-RAY DIFFRACTIONr_angle_other_deg0.923.0038152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69824.559204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00115839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1761522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025648
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02993
X-RAY DIFFRACTIONr_nbd_refined0.2190.2745
X-RAY DIFFRACTIONr_nbd_other0.1990.23408
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22376
X-RAY DIFFRACTIONr_nbtor_other0.0860.22757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2400
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2771.53999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52225100
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.56232151
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5084.51628
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.53 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 171
Rwork0.267 3603
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)
10.66870.38170.58842.04011.60382.3794-0.06930.0988-0.0295-0.26380.2507-0.2192-0.20160.2669-0.1814-0.0195-0.0405-0.00110.0191-0.0406-0.024532.195-9.561-5.28
20.8245-0.031-0.1340.9464-0.24451.4575-0.0270.01390.02270.0924-0.0245-0.0928-0.11160.05030.0515-0.04460.0016-0.06610.0051-0.0072-0.024229.9272.89124.126
34.31831.4337-0.51752.3985-0.77782.065-0.2831-0.37430.05790.07420.13730.0156-0.05950.23650.14580.03460.026-0.1053-0.028-0.0115-0.09911.2832.72555.976
41.13161.1248-1.39071.7984-1.4212.5466-0.15440.1704-0.0311-0.16120.19940.06190.3185-0.2619-0.045-0.038-0.0247-0.05820.02960.004-0.025812.045-11.1120.203
51.0437-0.28680.10672.31091.22561.2187-0.0829-0.11140.11970.13570.0663-0.1147-0.0583-0.04160.01660.03170.0025-0.0733-0.0169-0.008-0.0601-2.1456.98347.645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1I37 - 192
2X-RAY DIFFRACTION2H1 - 113
3X-RAY DIFFRACTION3H114 - 213
4X-RAY DIFFRACTION4L1 - 107
5X-RAY DIFFRACTION5L108 - 213

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