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- PDB-3qb1: Interleukin-2 mutant D10 -

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Basic information

Entry
Database: PDB / ID: 3qb1
TitleInterleukin-2 mutant D10
ComponentsInterleukin-2Interleukin 2
KeywordsCYTOKINE / high affinity IL-2 cytokine
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsLevin, A.M. / Bates, D.L. / Ring, A.M. / Lin, J.T. / Su, L. / Krieg, C. / Bowman, G.R. / Novick, P. / Pande, V.S. / Khort, H.E. ...Levin, A.M. / Bates, D.L. / Ring, A.M. / Lin, J.T. / Su, L. / Krieg, C. / Bowman, G.R. / Novick, P. / Pande, V.S. / Khort, H.E. / Boyman, O. / Fathman, C.G. / Garcia, K.C.
CitationJournal: Nature / Year: 2012
Title: Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'
Authors: Levin, A.M. / Bates, D.L. / Ring, A.M. / Krieg, C. / Lin, J.T. / Su, L. / Moraga, I. / Raeber, M.E. / Bowman, G.R. / Novick, P. / Pande, V.S. / Fathman, C.G. / Boyman, O. / Garcia, K.C.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Interleukin-2
D: Interleukin-2
E: Interleukin-2
F: Interleukin-2
G: Interleukin-2
H: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)125,8178
Polymers125,8178
Non-polymers00
Water0
1
A: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.873, 75.019, 76.812
Angle α, β, γ (deg.)101.460, 102.290, 104.310
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a single chain ID

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Components

#1: Protein
Interleukin-2 / Interleukin 2 / IL-2 / T-cell growth factor / TCGF


Mass: 15727.153 Da / Num. of mol.: 8 / Mutation: Q74H, L80F, R81D, L85V, I86V, I92F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Plasmid: pAcGP67A / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 50 mM HEPES, 200 mM NaCl, 30% PEG-4000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2010
RadiationMonochromator: Si 111 Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 20383 / Num. obs: 20383 / % possible obs: 99 % / Observed criterion σ(F): 1.98 / Observed criterion σ(I): 2.01 / Redundancy: 2.2 % / Rmerge(I) obs: 0.056 / Χ2: 1.031 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.212.20.4420010.979198.4
3.21-3.342.20.33920460.988198.6
3.34-3.492.20.23120470.98198.7
3.49-3.682.20.14520291198.9
3.68-3.912.20.09420341.031198.8
3.91-4.212.20.06320350.941199
4.21-4.632.20.04620521.004199.2
4.63-5.32.20.04220321.067199.3
5.3-6.672.20.05520481.272199.4
6.67-502.20.02420591.048199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_621refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1M47

1m47


Resolution: 3.1→42.4 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7693 / SU ML: 0.39 / σ(F): 1.98 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1043 5.13 %Random
Rwork0.221 ---
obs0.224 20351 97.38 %-
all-20351 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.203 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 214.13 Å2 / Biso mean: 84.5827 Å2 / Biso min: 40.73 Å2
Baniso -1Baniso -2Baniso -3
1-18.0388 Å27.1557 Å27.0408 Å2
2--2.0508 Å26.2691 Å2
3----12.4099 Å2
Refinement stepCycle: LAST / Resolution: 3.1→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7786 0 0 0 7786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097923
X-RAY DIFFRACTIONf_angle_d1.02310667
X-RAY DIFFRACTIONf_chiral_restr0.0661270
X-RAY DIFFRACTIONf_plane_restr0.0051318
X-RAY DIFFRACTIONf_dihedral_angle_d14.2562960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0876-3.25040.33481280.31182501262988
3.2504-3.45390.34031440.2782796294099
3.4539-3.72050.2741510.25172828297999
3.7205-4.09460.29981600.21182752291299
4.0946-4.68640.20761510.19042832298399
4.6864-5.90190.28041450.22222795294099
5.9019-42.40430.23761640.20392804296899

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