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- PDB-8q5r: HpARI bound to mouse IL-33 -

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Basic information

Entry
Database: PDB / ID: 8q5r
TitleHpARI bound to mouse IL-33
Components
  • Alarmin release inhibitor
  • Interleukin-33
KeywordsIMMUNOSUPPRESSANT / Helminth / IL-33 / anti-allergy / anti-inflammatory
Function / homology
Function and homology information


regulation of response to cytokine stimulus / interleukin-33 binding / Interleukin-33 signaling / interleukin-33 receptor binding / negative regulation of macrophage proliferation / : / : / positive regulation of cellular defense response / regulation of cytokine activity / positive regulation of MHC class I biosynthetic process ...regulation of response to cytokine stimulus / interleukin-33 binding / Interleukin-33 signaling / interleukin-33 receptor binding / negative regulation of macrophage proliferation / : / : / positive regulation of cellular defense response / regulation of cytokine activity / positive regulation of MHC class I biosynthetic process / negative regulation of immunoglobulin production / microglial cell activation involved in immune response / negative regulation of T-helper 1 type immune response / negative regulation of inflammatory response to wounding / negative regulation of leukocyte migration / antibacterial innate immune response / PIP3 activates AKT signaling / microglial cell proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / interleukin-33-mediated signaling pathway / positive regulation of type 2 immune response / positive regulation of interleukin-13 production / response to host immune response / positive regulation of interleukin-5 production / Ub-specific processing proteases / macrophage activation involved in immune response / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / type 2 immune response / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / negative regulation of type II interferon production / macrophage differentiation / positive regulation of oligodendrocyte differentiation / transport vesicle / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / cytokine activity / positive regulation of interleukin-6 production / response to wounding / cellular response to mechanical stimulus / positive regulation of inflammatory response / protein import into nucleus / positive regulation of tumor necrosis factor production / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / chromosome / gene expression / defense response to virus / positive regulation of gene expression / host cell nucleus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Interleukin-33 / : / Interleukin 33 / Sushi/SCR/CCP superfamily
Similarity search - Domain/homology
Alarmin release inhibitor / Interleukin-33
Similarity search - Component
Biological speciesMus musculus (house mouse)
Heligmosomoides bakeri (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJamwal, A. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust221914/Z/20/Z United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for IL-33 recognition and its antagonism by the helminth effector protein HpARI2.
Authors: Jamwal, A. / Colomb, F. / McSorley, H.J. / Higgins, M.K.
History
DepositionAug 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: 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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-33
B: Alarmin release inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6065
Polymers43,4462
Non-polymers1603
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-23 kcal/mol
Surface area16270 Å2
Unit cell
Length a, b, c (Å)149.779, 35.755, 61.289
Angle α, β, γ (deg.)90.000, 92.070, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-340-

HOH

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Components

#1: Protein Interleukin-33


Mass: 17569.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il33 / Production host: Homo sapiens (human) / References: UniProt: Q8BVZ5
#2: Protein Alarmin release inhibitor


Mass: 25876.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heligmosomoides bakeri (invertebrata) / Gene: ARI / Production host: Homo sapiens (human) / References: UniProt: A0A3P7XL18
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 6.8 and 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→48.26 Å / Num. obs: 19343 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 1046 / CC1/2: 0.728

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Processing

Software
NameVersionClassification
BUSTERrefinement
PDB_EXTRACT3.28data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.26 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1540 7.97 %
Rwork0.18 --
obs0.1839 19312 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.48 Å2 / Biso mean: 62.4777 Å2 / Biso min: 27.03 Å2
Refinement stepCycle: final / Resolution: 2.1→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 9 103 2535
Biso mean--71.73 56.74 -
Num. residues----313
Refinement TLS params.Method: refined / Origin x: 10.4685 Å / Origin y: -3.6637 Å / Origin z: -12.1678 Å
111213212223313233
T0.4001 Å20.0177 Å20.0158 Å2-0.2661 Å2-0.0241 Å2--0.3401 Å2
L2.4349 °20.4153 °20.6423 °2-1.5937 °2-0.0446 °2--2.9399 °2
S-0.0706 Å °0.1574 Å °0.0751 Å °0.0087 Å °-0.024 Å °-0.1323 Å °-0.0655 Å °-0.2302 Å °0.0895 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA111 - 266
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allB64 - 237
4X-RAY DIFFRACTION1allS1 - 142
5X-RAY DIFFRACTION1allC1 - 301

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