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- PDB-7m2g: INTERLEUKIN-2 (human) mutant P65K, C125S -

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Basic information

Entry
Database: PDB / ID: 7m2g
TitleINTERLEUKIN-2 (human) mutant P65K, C125S
ComponentsInterleukin-2
KeywordsCYTOKINE / CYTOKINE IL-2 mutein human
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 / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsPtacin, J.L. / Milla, M.E. / Steinbacher, S. / Maskos, K. / Thomsen, M.
CitationJournal: Nat Commun / Year: 2021
Title: An engineered IL-2 reprogrammed for anti-tumor therapy using a semi-synthetic organism.
Authors: Ptacin, J.L. / Caffaro, C.E. / Ma, L. / San Jose Gall, K.M. / Aerni, H.R. / Acuff, N.V. / Herman, R.W. / Pavlova, Y. / Pena, M.J. / Chen, D.B. / Koriazova, L.K. / Shawver, L.K. / Joseph, I.B. / Milla, M.E.
History
DepositionMar 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)15,6403
Polymers15,4521
Non-polymers1882
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.501, 73.501, 76.965
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

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Components

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


Mass: 15451.981 Da / Num. of mol.: 1 / Fragment: IL2 / Mutation: P65K, C125S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60568
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.55 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.75
Details: 1.75M (NH4)2SO4, 0.10 M HEPES/NaOH pH=7.75 at a protein concentration of 37 mg/ml.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999965 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999965 Å / Relative weight: 1
ReflectionResolution: 1.788→53.16 Å / Num. obs: 20517 / % possible obs: 100 % / Redundancy: 16.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.013 / Rrim(I) all: 0.05 / Rsym value: 0.048 / Net I/σ(I): 27.8
Reflection shellResolution: 1.788→1.819 Å / Redundancy: 15.7 % / Rmerge(I) obs: 1.866 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2930 / CC1/2: 0.835 / Rpim(I) all: 0.358 / Rrim(I) all: 1.439 / Rsym value: 1.866 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.27data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qb1

3qb1


Resolution: 1.79→53.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.969 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 1964 9.6 %RANDOM
Rwork0.1922 ---
obs0.1958 18553 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.42 Å2 / Biso mean: 59.513 Å2 / Biso min: 28.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---1.27 Å20 Å2
3---2.54 Å2
Refinement stepCycle: final / Resolution: 1.79→53.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 9 101 1173
Biso mean--81.62 61.62 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191150
X-RAY DIFFRACTIONr_bond_other_d0.0040.021121
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9761565
X-RAY DIFFRACTIONr_angle_other_deg1.25332588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29525.68651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62215225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.23154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021304
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02256
LS refinement shellResolution: 1.79→1.835 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.32 146 -
Rwork0.316 1333 -
obs--100 %
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)
13.38-0.3423-2.1013.77581.261112.2172-0.0902-0.29390.00080.42740.01590.08230.4132-0.13940.07440.05820.0049-0.00060.0587-0.00760.0449-24.741-16.3535.863
23.9748-1.4363-2.04192.6595-0.80976.17580.10190.22090.2611-0.1955-0.13910.0352-0.0563-0.57220.03710.08760.04230.02920.11080.01820.0966-27.481-7.421-2.684
33.7824-2.31821.61635.9227-2.62499.32010.016-0.14410.57080.29450.1049-0.4549-0.80170.1084-0.1210.0813-0.01590.02980.0386-0.01890.1138-17.447-7.8992.233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 51
2X-RAY DIFFRACTION2A52 - 121
3X-RAY DIFFRACTION3A122 - 153

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