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- PDB-7fch: IL-18Rbeta TIR domain -

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Basic information

Entry
Database: PDB / ID: 7fch
TitleIL-18Rbeta TIR domain
ComponentsInterleukin-18 receptor accessory protein
KeywordsIMMUNE SYSTEM / IL-18Rbeta / TIR domain / receptor protein
Function / homology
Function and homology information


interleukin-18 receptor activity / interleukin-18 receptor complex / Interleukin-18 signaling / positive regulation of natural killer cell mediated cytotoxicity / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / neutrophil activation / NAD+ nucleosidase activity, cyclic ADP-ribose generating / coreceptor activity / positive regulation of NF-kappaB transcription factor activity ...interleukin-18 receptor activity / interleukin-18 receptor complex / Interleukin-18 signaling / positive regulation of natural killer cell mediated cytotoxicity / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / neutrophil activation / NAD+ nucleosidase activity, cyclic ADP-ribose generating / coreceptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to hydrogen peroxide / adaptive immune response / cell population proliferation / immune response / inflammatory response / cell surface / plasma membrane
Similarity search - Function
IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype / Immunoglobulin ...IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-18 receptor accessory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.883 Å
AuthorsWang, X. / Zhou, J.
CitationJournal: Iscience / Year: 2022
Title: Structural basis of the IL-1 receptor TIR domain-mediated IL-1 signaling
Authors: Zhou, J. / Xiao, Y. / Ren, Y. / Ge, J. / Wang, X.
History
DepositionJul 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-18 receptor accessory protein
B: Interleukin-18 receptor accessory protein
C: Interleukin-18 receptor accessory protein
D: Interleukin-18 receptor accessory protein


Theoretical massNumber of molelcules
Total (without water)76,3124
Polymers76,3124
Non-polymers00
Water3,135174
1
A: Interleukin-18 receptor accessory protein

C: Interleukin-18 receptor accessory protein


Theoretical massNumber of molelcules
Total (without water)38,1562
Polymers38,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area1330 Å2
ΔGint-12 kcal/mol
Surface area13990 Å2
MethodPISA
2
B: Interleukin-18 receptor accessory protein
D: Interleukin-18 receptor accessory protein


Theoretical massNumber of molelcules
Total (without water)38,1562
Polymers38,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-14 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.760, 161.074, 52.164
Angle α, β, γ (deg.)90.000, 112.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Interleukin-18 receptor accessory protein / IL-18 receptor accessory protein / IL-18RAcP


Mass: 19078.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18RAP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O95256, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium tartrate dibasic, pH 6.25, 20% w/v PEG3350, 3% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.48
ReflectionResolution: 1.88→50 Å / Num. obs: 46801 / % possible obs: 95.61 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 1.88→1.92 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 4060

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FCC

7fcc


Resolution: 1.883→48.214 Å / Cross valid method: THROUGHOUT / σ(F): 9.37 / Phase error: 28.32 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2226 2316 4.96 %
Rwork0.1864 44424 -
obs0.2 46711 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.79 Å2 / Biso mean: 35.5059 Å2 / Biso min: 17.23 Å2
Refinement stepCycle: final / Resolution: 1.883→48.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 0 174 4790
Biso mean---37.01 -
Num. residues----572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8838-1.92470.36811050.3296234076
1.9247-1.96940.3261480.311261886
1.9694-2.01860.3181380.318271689
2.0186-2.07320.37641200.3118275091
2.0732-2.13410.29861350.2986273491
2.1341-2.20290.3211640.2961276890
2.2029-2.28160.30281440.2791273291
2.2816-2.37280.35411200.2582282492
2.3728-2.48060.29011120.2631289894
2.4806-2.61120.31211460.2556280793
2.6112-2.77440.25671430.2361283694
2.7744-2.9880.23861570.2121286294
2.988-3.28770.21391620.183285894
3.2877-3.76090.22711300.146290595
3.7609-4.7290.17951570.1223289094
4.729-100.20861670.1492288694

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