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- PDB-1m4c: Crystal Structure of Human Interleukin-2 -

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Basic information

Entry
Database: PDB / ID: 1m4c
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsArkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / McDowell, R.S. ...Arkin, M.A. / 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.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Binding of small molecules to an adaptive protein-protein interface
Authors: Arkin, M.A. / 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 1.3Oct 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
B: interleukin-2


Theoretical massNumber of molelcules
Total (without water)30,8722
Polymers30,8722
Non-polymers00
Water00
1
A: interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,4361
Polymers15,4361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,4361
Polymers15,4361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.181, 48.597, 79.209
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / Refine code: 2

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRAA6 - 1316 - 131
2LEUBB6 - 1326 - 132

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Components

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


Mass: 15435.979 Da / Num. of mol.: 2
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

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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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 12, 2000 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / Num. all: 8581 / Num. obs: 8581 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 4.1 / Num. unique all: 619 / Rsym value: 0.259 / % possible all: 58.1

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Processing

Software
NameVersionClassification
d*TREKdata reduction
AMoREphasing
REFMAC5refinement
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→10 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.858 / SU B: 10.174 / SU ML: 0.226 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.93 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: tight NCS restraints used throughout refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.33287 438 4.9 %RANDOM
Rwork0.28617 ---
all0.28832 8581 --
obs0.28832 8581 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.019 Å2
Baniso -1Baniso -2Baniso -3
1--3.56 Å20 Å2-0.41 Å2
2--0.42 Å20 Å2
3---3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 0 0 1872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0221898
X-RAY DIFFRACTIONr_angle_refined_deg0.7131.9882555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.7383223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03715403
X-RAY DIFFRACTIONr_chiral_restr0.0550.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021324
X-RAY DIFFRACTIONr_nbd_refined0.240.3826
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.565
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.53
X-RAY DIFFRACTIONr_mcbond_it1.6552.51141
X-RAY DIFFRACTIONr_mcangle_it2.90951856
X-RAY DIFFRACTIONr_scbond_it1.4722.5757
X-RAY DIFFRACTIONr_scangle_it2.455699
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 932 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.010.05
tight thermal0.030.5
LS refinement shellResolution: 2.4→2.479 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.479 26 -
Rwork0.36 593 -
obs-619 58.1 %

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