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- PDB-7ox6: Solution structure of human interleukin-9 -

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Basic information

Entry
Database: PDB / ID: 7ox6
TitleSolution structure of human interleukin-9
ComponentsInterleukin-9
KeywordsCYTOKINE / four-helical bundle / IL-9
Function / homology
Function and homology information


interleukin-9 receptor binding / Interleukin-9 signaling / interleukin-9-mediated signaling pathway / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / immunoglobulin mediated immune response / B cell proliferation / B cell differentiation / cytokine activity / growth factor activity ...interleukin-9 receptor binding / Interleukin-9 signaling / interleukin-9-mediated signaling pathway / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / immunoglobulin mediated immune response / B cell proliferation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of cell growth / inflammatory response / positive regulation of cell population proliferation / extracellular space / extracellular region
Similarity search - Function
Interleukin-9 / Interleukin-7/Interleukin-9, conserved site / Interleukin-7 and -9 signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSavvides, S.N. / Tripsianes, K. / De Vos, T. / Papageorgiou, A. / Evangelidis, T.
CitationJournal: Biorxiv / Year: 2022
Title: Structural basis for the mechanism and antagonism of receptor signaling mediated by Interleukin-9 (IL-9)
Authors: De Vos, T. / Godar, M. / Bick, F. / Papageorgiou, A.C. / Evangelidis, T. / Markovic, I. / Mortier, E. / Dumoutier, L. / Tripsianes, K. / Blanchetot, C. / Savvides, S.N.
History
DepositionJun 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-9


Theoretical massNumber of molelcules
Total (without water)14,5511
Polymers14,5511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7300 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Interleukin-9 / IL-9 / Cytokine P40 / T-cell growth factor P40


Mass: 14551.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15248
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D HC(CC TOCSY(CO))NH
121isotropic14D 13C,15N edited HMQC-NOESY-HSQC
131isotropic14D 13C,13C edited HMQC-NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 60 mg/mL [U-13C; U-15N] Interleukin-9, 90% H2O/10% D2O
Label: hIL-9 / Solvent system: 90% H2O/10% D2O
SampleConc.: 60 mg/mL / Component: Interleukin-9 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 mM / Label: Buffer_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
4D-CHAINSEvangelidis and Tripsianeschemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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