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- PDB-2l3o: Solution structure of murine interleukin 3 -

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Basic information

Entry
Database: PDB / ID: 2l3o
TitleSolution structure of murine interleukin 3
ComponentsInterleukin 3
KeywordsCYTOKINE / Murine Interleukin-3
Function / homology
Function and homology information


regulation of protein dephosphorylation / interleukin-3 receptor binding / positive regulation of myeloid leukocyte differentiation / negative regulation of mast cell apoptotic process / positive regulation of mast cell proliferation / myeloid cell apoptotic process / activation of Janus kinase activity / interleukin-3-mediated signaling pathway / regulation of glycolytic process / monocyte differentiation ...regulation of protein dephosphorylation / interleukin-3 receptor binding / positive regulation of myeloid leukocyte differentiation / negative regulation of mast cell apoptotic process / positive regulation of mast cell proliferation / myeloid cell apoptotic process / activation of Janus kinase activity / interleukin-3-mediated signaling pathway / regulation of glycolytic process / monocyte differentiation / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / response to hormone / negative regulation of autophagy / cytokine activity / regulation of cell growth / positive regulation of JNK cascade / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / regulation of gene expression / response to hypoxia / immune response / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space
Similarity search - Function
Interleukin-3 / Interleukin-3 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Interleukin-3 / Interleukin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsYao, S. / Young, I.G. / Norton, R.S. / Murphy, J.M.
CitationJournal: Biochemistry / Year: 2011
Title: Murine interleukin-3: structure, dynamics, and conformational heterogeneity in solution.
Authors: Yao, S. / Young, I.G. / Norton, R.S. / Murphy, J.M.
History
DepositionSep 20, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin 3


Theoretical massNumber of molelcules
Total (without water)14,3071
Polymers14,3071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200on the basis of stereochemistry and energy considerations
RepresentativeModel #1closest to the average

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Components

#1: Protein Interleukin 3 /


Mass: 14307.247 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-156 / Mutation: C105A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il3, mCG_13767, mIL-3, RP23-309E16.5-001 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus / References: UniProt: Q5SX77, UniProt: P01586*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-15N HSQC
1413D 1H-15N NOESY
1522D 1H-15N HSQC
1622D 1H-13C HSQC
1723D HNCO
1823D HNCA
1923D HN(CO)CA
11023D CBCA(CO)NH
11123D HN(CA)CB
11223D (H)CCH-TOCSY
11323D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.15 mM [U-100% 15N] mIL-3-1, 20 mM potassium phosphate-2, 95% H2O/5% D2O95% H2O/5% D2O
20.3 mM [U-100% 13C; U-100% 15N] mIL-3-3, 20 mM potassium phosphate-4, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.15 mMmIL-3-1[U-100% 15N]1
20 mMpotassium phosphate-21
0.3 mMmIL-3-3[U-100% 13C; U-100% 15N]2
20 mMpotassium phosphate-42
Sample conditionsIonic strength: 0.020 / pH: 6.7 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance5001
Bruker AvanceBrukerAvance8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPIN1.3Bruker Biospincollection
TOPSPIN1.3Bruker Biospinprocessing
XEASY1.3Bartels et al.chemical shift assignment
XEASY1.3Bartels et al.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR_NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: on the basis of stereochemistry and energy considerations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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