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- PDB-4nem: Small molecular fragment bound to crystal contact interface of In... -

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Basic information

Entry
Database: PDB / ID: 4nem
TitleSmall molecular fragment bound to crystal contact interface of Interleukin-2
ComponentsInterleukin-2Interleukin 2
KeywordsIMMUNE SYSTEM / fragment mapping / crystal contact / cytokine / Interleukin-2 / helixbundle / CD25 / extracellular
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) / positive regulation of isotype switching to IgG isotypes / leukocyte activation involved in immune response / interleukin-2-mediated signaling pathway / natural killer cell activation / activated T cell proliferation / positive regulation of regulatory T cell differentiation / protein kinase C-activating G protein-coupled receptor signaling pathway / kinase activator activity / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / positive regulation of immunoglobulin 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 / transcription by RNA polymerase II / adaptive immune response / 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
Chem-2JY / Interleukin-2 / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.934 Å
AuthorsJehle, S. / Brenke, R. / Vajda, S. / Allen, K.N. / Kozakov, D.
CitationJournal: To be Published
Title: Small molecular fragments bound to binding energy hot-spot in crystal contact interface of Interleukin-2
Authors: Jehle, S. / Brenke, R. / Vajda, S. / Allen, K.N. / Kozakov, D.
History
DepositionOct 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: 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-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4382
Polymers15,1511
Non-polymers2871
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.709, 48.544, 79.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interleukin-2 / Interleukin 2


Mass: 15150.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6QWN0, UniProt: P60568*PLUS
#2: Chemical ChemComp-2JY / 5-[(2,3-dichlorophenoxy)methyl]furan-2-carboxylic acid


Mass: 287.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8Cl2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 34% PEG 8K, 0.1 M NaOAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 9626 / Num. obs: 9626 / % possible obs: 99.23 % / Observed criterion σ(F): 24.56 / Observed criterion σ(I): 7.16 / Rsym value: 0.073

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.934→41.468 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 30.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 462 4.8 %
Rwork0.2069 --
obs0.2093 9625 99.22 %
all-9626 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.934→41.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 18 15 968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006967
X-RAY DIFFRACTIONf_angle_d0.9421302
X-RAY DIFFRACTIONf_dihedral_angle_d17.59370
X-RAY DIFFRACTIONf_chiral_restr0.038157
X-RAY DIFFRACTIONf_plane_restr0.003158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9335-2.21330.2841740.20572951X-RAY DIFFRACTION99
2.2133-2.78840.29551330.23933047X-RAY DIFFRACTION100
2.7884-41.4780.24271550.1973165X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.4172-0.5671.90832.44060.01293.7355-0.21970.27840.502-0.08320.05940.00380.0275-0.17580.19550.3069-0.02680.01060.2325-0.01990.3115-6.32257.7914.4082
22.47-1.3173-0.21957.13133.23954.7416-0.0886-0.51650.59051.1246-0.2853-0.4809-0.2425-0.23070.39230.4695-0.0001-0.07710.3972-0.06090.495613.1539-0.40124.9119
32.27990.25991.63451.71680.43793.1409-0.22660.4375-0.0695-0.47250.04710.0051-0.4511-0.25490.1380.43910.02080.00020.5881-0.15040.37791.3362-7.52738.6243
46.809-1.46153.22384.7964-1.48487.1633-0.0668-0.7285-1.12350.14060.32310.48430.7336-0.9252-0.11030.32920.00940.08080.363-0.01840.4395-3.9638-6.548816.3851
55.7139-1.84671.6483.8226-0.58842.7744-0.0805-0.9109-0.24730.1470.0084-0.24790.3469-0.06260.25410.33580.03130.01680.44460.04120.4706-7.538-0.626521.1123
60.12070.03140.22413.11871.1383.1888-0.42650.7497-0.7415-0.71030.17780.22120.32280.02960.19560.5833-0.06410.06650.4522-0.17320.5028-0.7102-10.92577.3892
75.5801-2.30483.36795.3133-2.47295.5707-0.09870.89710.2289-0.4453-0.1063-0.3121-0.22470.14530.13650.3596-0.01210.0240.41140.01920.2582-0.84963.42068.1925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:28 )A6 - 28
2X-RAY DIFFRACTION2( CHAIN A AND RESID 29:41 )A29 - 41
3X-RAY DIFFRACTION3( CHAIN A AND RESID 42:52 )A42 - 52
4X-RAY DIFFRACTION4( CHAIN A AND RESID 53:71 )A53 - 71
5X-RAY DIFFRACTION5( CHAIN A AND RESID 72:96 )A72 - 96
6X-RAY DIFFRACTION6( CHAIN A AND RESID 97:113 )A97 - 113
7X-RAY DIFFRACTION7( CHAIN A AND RESID 114:133 )A114 - 133

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