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- PDB-2kll: Solution structure of human interleukin-33 -

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Basic information

Entry
Database: PDB / ID: 2kll
TitleSolution structure of human interleukin-33
ComponentsInterleukin-33
KeywordsCYTOKINE / interleukin / beta-trefoil / Polymorphism / Secreted
Function / homology
Function and homology information


interleukin-33 receptor binding / negative regulation of macrophage proliferation / : / : / positive regulation of cellular defense response / Interleukin-33 signaling / 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 ...interleukin-33 receptor binding / negative regulation of macrophage proliferation / : / : / positive regulation of cellular defense response / Interleukin-33 signaling / 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 / microglial cell proliferation / interleukin-33-mediated signaling pathway / positive regulation of type 2 immune response / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / positive regulation of neuroinflammatory 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 cytokine production / 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 / PIP3 activates AKT signaling / chromosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / gene expression / defense response to virus / Ub-specific processing proteases / intracellular membrane-bounded organelle / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Interleukin-33 / : / Interleukin 33 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLingel, A. / Fairbrother, W.
CitationJournal: Structure / Year: 2009
Title: Structure of IL-33 and its interaction with the ST2 and IL-1RAcP receptors--insight into heterotrimeric IL-1 signaling complexes.
Authors: Lingel, A. / Weiss, T.M. / Niebuhr, M. / Pan, B. / Appleton, B.A. / Wiesmann, C. / Bazan, J.F. / Fairbrother, W.J.
History
DepositionJul 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-33


Theoretical massNumber of molelcules
Total (without water)18,1591
Polymers18,1591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Interleukin-33 / IL-33 / Interleukin-1 family member 11 / IL-1F11 / Nuclear factor from high endothelial venules / NF-HEV


Mass: 18159.301 Da / Num. of mol.: 1 / Fragment: UNP residues 110-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL33, C9orf26, IL1F11, NFHEV / Production host: Escherichia coli (E. coli) / References: UniProt: O95760

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1243D 1H-13C NOESY
1313D HNHA
1422D 1H-1H NOESY
1533D HNCA
1633D HN(CA)CB
1733D CBCA(CO)NH
1833D C(CO)NH
1933D H(CCO)NH
11043D (H)CCH-TOCSY
11112D 1H-15N HSQC
11232D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] Interleukin-33, 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM beta-mercaptoethanol, 95% H2O/5% D2O95% H2O/5% D2O
21 mM Interleukin-33, 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM [U-100% 2H] beta-mercaptoethanol, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] Interleukin-33, 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM beta-mercaptoethanol, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-100% 13C; U-100% 15N] Interleukin-33, 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM [U-100% 2H] beta-mercaptoethanol, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMInterleukin-33[U-100% 15N]1
20 mMsodium phosphate1
100 mMsodium chloride1
5 mMbeta-mercaptoethanol1
1 mMInterleukin-332
20 mMsodium phosphate2
100 mMsodium chloride2
5 mMbeta-mercaptoethanol[U-100% 2H]2
1 mMInterleukin-33[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate3
100 mMsodium chloride3
5 mMbeta-mercaptoethanol3
1 mMInterleukin-33[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate4
100 mMsodium chloride4
5 mMbeta-mercaptoethanol[U-100% 2H]4
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBrukercollection
CCPNCCPNdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
MOLMOLKoradi, Billeter and Wuthrichdisplay
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Distance restraints were derived from 15N- or 13C-resolved 3D NOESY experiments and a 2D homonuclear 1H NOESY experiment. Restraints for the backbone angles phi and psi were derived from ...Details: Distance restraints were derived from 15N- or 13C-resolved 3D NOESY experiments and a 2D homonuclear 1H NOESY experiment. Restraints for the backbone angles phi and psi were derived from TALOS. Stereospecific assignments of Leu, Val methyl groups were obtained using a 10% fractionally 13C-labeled sample. For the definition of H-bonds, slowly exchanging amide protons were identified from 1H, 15N correlation experiments after redissolving lyophilized protein in D2O.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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