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- PDB-7ra9: Designed StabIL-2 seq1 -

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Basic information

Entry
Database: PDB / ID: 7ra9
TitleDesigned StabIL-2 seq1
ComponentsInterleukin-2
KeywordsCYTOKINE / synthetic protein
Function / homology
Function and homology information


kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / negative regulation of lymphocyte proliferation / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling ...kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / negative regulation of lymphocyte proliferation / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling / 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 / cell surface receptor signaling pathway via STAT / kinase activator activity / natural killer cell activation / Interleukin-2 signaling / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / positive regulation of inflammatory response / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / carbohydrate binding / positive regulation of cell growth / response to ethanol / phospholipase C-activating G protein-coupled receptor signaling pathway / 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
PHOSPHATE ION / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJude, K.M. / Chu, A.E. / Huang, P.-S. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI051321 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Interleukin-2 superkines by computational design.
Authors: Ren, J. / Chu, A.E. / Jude, K.M. / Picton, L.K. / Kare, A.J. / Su, L. / Montano Romero, A. / Huang, P.S. / Garcia, K.C.
History
DepositionJun 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6575
Polymers15,1341
Non-polymers5234
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, isothermal titration calorimetry, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.588, 46.588, 234.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

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


Mass: 15133.517 Da / Num. of mol.: 1
Mutation: G27M, I28L, K32D, M39L, E52S, V69A, L72A, Q74G, S75D, K76D, N77P, F78K, H79T, L80I, delta81-82, L85V, I86V, I92F, V115I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P60568
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2 M Li2SO4, 0.1 M CAPS pH 10.5, 1.2 M NaH2PO4, and 0.8 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.2→40.35 Å / Num. obs: 8217 / % possible obs: 95.97 % / Redundancy: 16.9 % / Biso Wilson estimate: 47.25 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.07409 / Rrim(I) all: 0.3092 / Rsym value: 0.2997 / Net I/σ(I): 5.78
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 0.57 / Num. unique obs: 697 / CC1/2: 0.266 / CC star: 0.648 / Rpim(I) all: 1.141 / Rrim(I) all: 3.606 / Rsym value: 3.411 / % possible all: 78.84

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122+SVNrefinement
XDSJan 31, 2020data reduction
XDSJan 31, 2020data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NEJ

4nej


Resolution: 2.2→40.35 Å / SU ML: 0.3426 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.5766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2927 809 10 %
Rwork0.2533 7285 -
obs0.2572 8094 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 30 34 1082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00141073
X-RAY DIFFRACTIONf_angle_d0.40691456
X-RAY DIFFRACTIONf_chiral_restr0.0319172
X-RAY DIFFRACTIONf_plane_restr0.0035177
X-RAY DIFFRACTIONf_dihedral_angle_d11.2222411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.41291170.37211055X-RAY DIFFRACTION87.2
2.34-2.520.37561340.30441211X-RAY DIFFRACTION99.7
2.52-2.770.31111240.30181119X-RAY DIFFRACTION91.2
2.77-3.170.33521380.2821247X-RAY DIFFRACTION99.86
3.17-3.990.25821430.23841268X-RAY DIFFRACTION98.95
4-40.350.27081530.22621385X-RAY DIFFRACTION98.27
Refinement TLS params.Method: refined / Origin x: 16.0715517893 Å / Origin y: 26.7229094276 Å / Origin z: 118.886961607 Å
111213212223313233
T0.271097606807 Å2-0.0042580636128 Å20.0466263353907 Å2-0.205530709092 Å20.00750748102563 Å2--0.44759572274 Å2
L3.48593641012 °2-1.07414825207 °21.72629901155 °2-2.39640446286 °2-0.636175004979 °2--6.5312198812 °2
S0.132470634827 Å °0.210528060329 Å °0.222457718781 Å °-0.0905256485594 Å °0.00908971219969 Å °-0.00599089336463 Å °-0.0545480936381 Å °0.0574608061065 Å °-0.0629623938231 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 10 through 135)

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