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- PDB-7fcc: IL-1RAcPb TIR domain -

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Basic information

Entry
Database: PDB / ID: 7fcc
TitleIL-1RAcPb TIR domain
ComponentsIsoform 4 of Interleukin-1 receptor accessory protein
KeywordsIMMUNE SYSTEM / IL-1RAcPb / TIR domain / receptor protein
Function / homology
Function and homology information


Interleukin-33 signaling / interleukin-33 receptor activity / Interleukin-36 pathway / interleukin-1 receptor activity / trans-synaptic signaling by trans-synaptic complex / Receptor-type tyrosine-protein phosphatases / regulation of postsynaptic density assembly / synaptic membrane adhesion / interleukin-33-mediated signaling pathway / positive regulation of interleukin-13 production ...Interleukin-33 signaling / interleukin-33 receptor activity / Interleukin-36 pathway / interleukin-1 receptor activity / trans-synaptic signaling by trans-synaptic complex / Receptor-type tyrosine-protein phosphatases / regulation of postsynaptic density assembly / synaptic membrane adhesion / interleukin-33-mediated signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / interleukin-1 receptor binding / positive regulation of synapse assembly / interleukin-1-mediated signaling pathway / positive regulation of interleukin-4 production / regulation of presynapse assembly / coreceptor activity / Interleukin-1 signaling / positive regulation of interleukin-6 production / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / inflammatory response / immune response / innate immune response / glutamatergic synapse / extracellular region / membrane / plasma membrane
Similarity search - Function
Interleukin-1 receptor type I/II / 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 ...Interleukin-1 receptor type I/II / 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-1 receptor accessory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.144 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: Isoform 4 of Interleukin-1 receptor accessory protein


Theoretical massNumber of molelcules
Total (without water)16,8271
Polymers16,8271
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8070 Å2
Unit cell
Length a, b, c (Å)34.632, 51.170, 78.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isoform 4 of Interleukin-1 receptor accessory protein / IL-1 receptor accessory protein


Mass: 16827.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RAP, C3orf13, IL1R3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9NPH3, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ISOFORM 4 FOUND IN UNP Q9NPH3.

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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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, pH 5.6, 20%w/v PEG4000, 20% v/v 2-propanol

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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: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.144→42.864 Å / Num. obs: 7875 / % possible obs: 97.25 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 13.4
Reflection shellResolution: 2.144→2.221 Å / Rmerge(I) obs: 0.757 / Num. unique obs: 663

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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: 1T3G

1t3g


Resolution: 2.144→42.864 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 419 5.33 %
Rwork0.1999 7449 -
obs0.2023 7868 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.48 Å2 / Biso mean: 34.5647 Å2 / Biso min: 20.49 Å2
Refinement stepCycle: final / Resolution: 2.144→42.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 0 54 1238
Biso mean---34.34 -
Num. residues----146
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.144-2.45380.27511270.2176229692
2.4538-3.09140.261360.22582517100
3.0914-100.22991560.18482636100

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