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- PDB-7fd3: IL-1RAPL2 TIR domain -

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Basic information

Entry
Database: PDB / ID: 7fd3
TitleIL-1RAPL2 TIR domain
ComponentsX-linked interleukin-1 receptor accessory protein-like 2
KeywordsIMMUNE SYSTEM / IL-1 family receptor protein / TIR domain
Function / homology
Function and homology information


interleukin-1, type II, blocking receptor activity / interleukin-1 receptor activity / Receptor-type tyrosine-protein phosphatases / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / regulation of presynapse assembly / central nervous system development / membrane => GO:0016020 / glutamatergic synapse / plasma membrane
Similarity search - Function
Interleukin-1 receptor type II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Interleukin-1 receptor type II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
X-linked interleukin-1 receptor accessory protein-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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 15, 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: X-linked interleukin-1 receptor accessory protein-like 2


Theoretical massNumber of molelcules
Total (without water)19,0491
Polymers19,0491
Non-polymers00
Water00
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 area8770 Å2
Unit cell
Length a, b, c (Å)51.141, 51.141, 184.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein X-linked interleukin-1 receptor accessory protein-like 2 / IL-1 receptor accessory protein-like 2 / IL-1-RAPL-2 / IL-1RAPL-2 / IL1RAPL-2


Mass: 19049.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RAPL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9NP60, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

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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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8% v/v tacsimate pH5.0, 12% w/v PEG3350

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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 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.99→49.29 Å / Num. obs: 5452 / % possible obs: 99.8 % / Redundancy: 24 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 19.6
Reflection shellResolution: 2.99→3.15 Å / Rmerge(I) obs: 1.716 / Num. unique obs: 515

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T3G

1t3g


Resolution: 2.99→49.29 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2825 268 4.93 %
Rwork0.2403 5169 -
obs0.2424 5437 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.97 Å2 / Biso mean: 87.415 Å2 / Biso min: 57.17 Å2
Refinement stepCycle: final / Resolution: 2.99→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 0 0 1289
Num. residues----155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.99-3.770.35171510.272324752626
3.77-49.290.25831170.231426942811

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