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- PDB-1m47: Crystal Structure of Human Interleukin-2 -

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Basic information

Entry
Database: PDB / ID: 1m47
TitleCrystal Structure of Human Interleukin-2
Componentsinterleukin-2
KeywordsCYTOKINE / four-helix bundle
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / natural killer cell activation / positive regulation of regulatory T cell differentiation / : / kinase activator activity / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / cell adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsArkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / Wells, J.A. ...Arkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / Wells, J.A. / McDowell, R.S. / Wells, J.A. / Braisted, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Binding of small molecules to an adaptive protein-protein interface.
Authors: Arkin, M.R. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / McDowell, R.S. / Wells, J.A. / Braisted, A.C.
History
DepositionJul 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Database references / Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6283
Polymers15,4361
Non-polymers1922
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.465, 84.777, 31.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein interleukin-2 / IL-2 / T-CELL GROWTH FACTOR / TCGF / ALDESLEUKIN


Mass: 15435.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60568
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mM1dropNaCl
225 mMammonium acetate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 27, 2002
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.95→10 Å / Num. all: 9522 / Num. obs: 9522 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 13.2
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.3 / Num. unique all: 855 / Rsym value: 0.391 / % possible all: 91.9
Reflection
*PLUS
Lowest resolution: 10 Å
Reflection shell
*PLUS
% possible obs: 91.9 %

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→15 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 2.4 / SU ML: 0.068 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24452 477 5 %RANDOM
Rwork0.21995 ---
all0.22118 9020 --
obs0.22118 9020 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--0.41 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.99→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 10 46 1055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0221023
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.991381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1683119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82615206
X-RAY DIFFRACTIONr_chiral_restr0.090.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02717
X-RAY DIFFRACTIONr_nbd_refined0.2360.3480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.554
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.52
X-RAY DIFFRACTIONr_mcbond_it2.0082.5609
X-RAY DIFFRACTIONr_mcangle_it3.6685991
X-RAY DIFFRACTIONr_scbond_it2.3812.5414
X-RAY DIFFRACTIONr_scangle_it4.0285390
LS refinement shellResolution: 1.99→2.054 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.319 45 -
Rwork0.282 810 -
obs-855 91.9 %
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection Rfree: 399 / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.25 Å2

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