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- PDB-7xcb: Crystal structure of the mouse interleukin-9 -

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Basic information

Entry
Database: PDB / ID: 7xcb
TitleCrystal structure of the mouse interleukin-9
ComponentsInterleukin-9
KeywordsCYTOKINE / interleukin / type I cytokine
Function / homology
Function and homology information


Interleukin-9 signaling / interleukin-9-mediated signaling pathway / positive regulation of interleukin-5 production / cytokine receptor binding / regulation of receptor signaling pathway via JAK-STAT / immunoglobulin mediated immune response / B cell proliferation / B cell differentiation / cytokine activity / growth factor activity / extracellular space
Similarity search - Function
Interleukin-9 / Interleukin-7/Interleukin-9, conserved site / Interleukin-7 and -9 signature.
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKim, J.W. / Lee, J.-O. / Park, S.M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019M3E5D6066058, 2017M3A9F6029753 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of the mouse interleukin-9
Authors: Kim, J.W. / Lee, J.-O. / Park, S.M.
History
DepositionMar 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 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-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8713
Polymers13,4281
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.500, 95.500, 105.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 13428.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: High five insect cells / Gene: Il9 / Plasmid: pFastBac1-HM / Cell line (production host): High five insect cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15247
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
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: 5.18 Å3/Da / Density % sol: 76.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1M citric acid(pH 3.5), 2.0M Ammonium sulfate / PH range: 3.5-4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2021
RadiationMonochromator: DCM Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 4255 / % possible obs: 99.7 % / Redundancy: 19.82 % / CC1/2: 0.85 / Rrim(I) all: 0.062 / Net I/σ(I): 41.13
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 18.55 % / Num. unique obs: 297 / CC1/2: 0.783 / Rrim(I) all: 0.228 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-P15247-F1

Resolution: 3.4→27.57 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 213 5.01 %213
Rwork0.2409 4040 --
obs0.2436 4253 99.63 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.74 Å2 / Biso min: 38.06 Å2
Refinement stepCycle: final / Resolution: 3.4→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms930 0 28 0 958
Biso mean--79.91 --
Num. residues----120
LS refinement shellResolution: 3.4→4.28 Å /
Rfactor% reflection
Rfree0.2554 -
Rwork0.2213 -
obs-100 %

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