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- PDB-4r6u: IL-18 receptor complex -

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Basic information

Entry
Database: PDB / ID: 4r6u
TitleIL-18 receptor complex
Components
  • Interleukin-18 receptor 1
  • Interleukin-18Interleukin 18
KeywordsIMMUNE SYSTEM / beta-trefoil fold / Ig-like fold
Function / homology
Function and homology information


interleukin-18 binding / interleukin-18 receptor activity / interleukin-18 receptor complex / interleukin-18 receptor binding / interleukin-1 receptor activity / T-helper 1 cell differentiation / 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 ...interleukin-18 binding / interleukin-18 receptor activity / interleukin-18 receptor complex / interleukin-18 receptor binding / interleukin-1 receptor activity / T-helper 1 cell differentiation / 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 / NAD+ nucleosidase activity / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / positive regulation of interleukin-13 production / natural killer cell mediated cytotoxicity / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / neutrophil activation / sleep / NAD+ nucleotidase, cyclic ADP-ribose generating / Interleukin-1 processing / positive regulation of NK T cell proliferation / Interleukin-37 signaling / triglyceride homeostasis / positive regulation of granulocyte macrophage colony-stimulating factor production / negative regulation of cold-induced thermogenesis / positive regulation of natural killer cell proliferation / 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 / signaling receptor activity / positive regulation of cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cellular response to lipopolysaccharide / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / inflammatory response / immune response / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Interleukin-1 receptor type I/II / Interleukin-18 / Interleukin-1 receptor family / Interleukin-1 family / Interleukin-1 / 18 / TIR domain / Cytokine IL1/FGF / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Interleukin-1 receptor type I/II / Interleukin-18 / Interleukin-1 receptor family / Interleukin-1 family / Interleukin-1 / 18 / TIR domain / Cytokine IL1/FGF / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-18 receptor 1 / Interleukin-18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWei, H. / Wang, X.
CitationJournal: Febs Lett. / Year: 2014
Title: Structural basis for the specific recognition of IL-18 by its alpha receptor.
Authors: Wei, H. / Wang, D. / Qian, Y. / Liu, X. / Fan, S. / Yin, H.S. / Wang, X.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Interleukin-18 receptor 1
A: Interleukin-18 receptor 1
B: Interleukin-18
D: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,41212
Polymers109,6424
Non-polymers1,7708
Water0
1
C: Interleukin-18 receptor 1
B: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7066
Polymers54,8212
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint6 kcal/mol
Surface area22850 Å2
MethodPISA
2
A: Interleukin-18 receptor 1
D: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7066
Polymers54,8212
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint7 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.392, 85.603, 88.117
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interleukin-18 receptor 1 / / IL-18R-1 / IL-18R1 / CD218 antigen-like family member A / CDw218a / IL1 receptor-related protein / ...IL-18R-1 / IL-18R1 / CD218 antigen-like family member A / CDw218a / IL1 receptor-related protein / IL-1Rrp / IL1R-rp


Mass: 36645.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18R1, IL1RRP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13478
#2: Protein Interleukin-18 / 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: 18175.467 Da / Num. of mol.: 2
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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20% PEG3350, 0.03 M citric acid, 0.07 M Bis-Tris propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2012
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 32392 / Num. obs: 31583 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.66 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J0S and 1ITB

1j0s

1itb


Resolution: 2.8→38.901 Å / SU ML: 0.49 / σ(F): 1.34 / Phase error: 32.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2817 1288 5.09 %
Rwork0.2331 --
obs0.2356 25300 96.93 %
all-26100 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→38.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6989 0 112 0 7101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137257
X-RAY DIFFRACTIONf_angle_d1.7999768
X-RAY DIFFRACTIONf_dihedral_angle_d17.5952714
X-RAY DIFFRACTIONf_chiral_restr0.0791098
X-RAY DIFFRACTIONf_plane_restr0.0091235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.43541490.32162684X-RAY DIFFRACTION98
2.9121-3.04460.35421490.32012702X-RAY DIFFRACTION99
3.0446-3.2050.36761270.27722706X-RAY DIFFRACTION98
3.205-3.40570.32311570.26992688X-RAY DIFFRACTION98
3.4057-3.66850.30011480.24922673X-RAY DIFFRACTION98
3.6685-4.03730.28311400.22842678X-RAY DIFFRACTION97
4.0373-4.62070.21961270.19292655X-RAY DIFFRACTION96
4.6207-5.81850.24221450.19932641X-RAY DIFFRACTION96
5.8185-38.9050.26331460.21962585X-RAY DIFFRACTION92
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)
10.3857-0.0945-0.15282.5109-0.45450.7934-0.0429-0.09670.00270.11080.0777-0.10140.08820.16160.00760.5132-0.0272-0.04240.6293-0.04610.5461237.9941-18.2775105.8764
22.26310.4968-0.03734.82-0.63742.71870.00020.1037-0.2591-0.0394-0.022-0.2130.01930.0112-0.00030.27530.047-0.00660.3815-0.0140.3736274.4672-5.1502105.2319
30.2465-0.0713-0.00132.8246-0.79681.24720.02230.06080.0272-0.15450.0018-0.1943-0.05620.1920.00660.4580.04090.03060.6253-0.00240.5559272.12873.6341112.617
41.5011-0.6333-0.15284.1123-0.53292.4596-0.0582-0.2790.06620.25030.05970.0354-0.16430.03640.00250.31610.0535-0.02230.48880.00460.3795238.5469-9.5478113.958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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