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- PDB-8soz: Structure of the complex formed by human interleukin-2 and scFv 602 -

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Basic information

Entry
Database: PDB / ID: 8soz
TitleStructure of the complex formed by human interleukin-2 and scFv 602
Components
  • 602 single chain fragment variable
  • Interleukin-2
KeywordsCYTOKINE / Complex / Antibody / Interleukin
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling ...kappa-type opioid receptor binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / 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 / kinase activator activity / positive regulation of regulatory T cell differentiation / natural killer cell activation / : / 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 tyrosine phosphorylation of STAT protein / positive regulation of B cell proliferation / 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 / carbohydrate binding / positive regulation of cell growth / 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: 1.64 Å
AuthorsGould, J.R. / Leonard, E.K. / Cao, S.D. / Spangler, J.B.
Funding support United States, 11items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH1810735 United States
Department of Defense (DOD, United States)W81XWH21P0031 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21CA249381 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)R01EB029455 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)R01EB029341 United States
V Foundation for Cancer ResearchV2018-005 United States
American Cancer SocietyPF-22-050-01-IBCD United States
Maryland Stem Cell Research Fund2019-MSCRFD-5039 United States
Emerson CollectiveCancer Research Fund United States
Willowcroft Foundation United States
Johns Hopkins UniversityCatalyst award United States
CitationJournal: JCI Insight / Year: 2024
Title: Engineered cytokine/antibody fusion proteins improve IL-2 delivery to pro-inflammatory cells and promote antitumor activity.
Authors: Leonard, E.K. / Tomala, J. / Gould, J.R. / Leff, M.I. / Lin, J.X. / Li, P. / Porter, M.J. / Johansen, E.R. / Thompson, L. / Cao, S.D. / Hou, S. / Henclova, T. / Huliciak, M. / Sargunas, P.R. ...Authors: Leonard, E.K. / Tomala, J. / Gould, J.R. / Leff, M.I. / Lin, J.X. / Li, P. / Porter, M.J. / Johansen, E.R. / Thompson, L. / Cao, S.D. / Hou, S. / Henclova, T. / Huliciak, M. / Sargunas, P.R. / Fabilane, C.S. / Vanek, O. / Kovar, M. / Schneider, B. / Raimondi, G. / Leonard, W.J. / Spangler, J.B.
History
DepositionApr 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 602 single chain fragment variable
A: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)41,2902
Polymers41,2902
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.192, 36.419, 64.189
Angle α, β, γ (deg.)90.00, 108.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 602 single chain fragment variable


Mass: 25425.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human)
#2: Protein Interleukin-2 / IL-2 / T-cell growth factor / TCGF


Mass: 15864.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: P60568
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
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: 1.8 Å3/Da / Density % sol: 31.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 15-30% PEG 3350, 0.1-0.35 ammonium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 30, 2023 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.64→61 Å / Num. obs: 37048 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 5.97
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 3555 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→32.6 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1839 4.93 %Random selection
Rwork0.219 ---
obs-37047 99.06 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 0 155 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092701
X-RAY DIFFRACTIONf_angle_d1.1483659
X-RAY DIFFRACTIONf_dihedral_angle_d6.319359
X-RAY DIFFRACTIONf_chiral_restr0.067423
X-RAY DIFFRACTIONf_plane_restr0.01457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.690.4011780.37013418X-RAY DIFFRACTION96.6
1.69-1.760.33911780.31273559X-RAY DIFFRACTION99.5
1.76-1.840.31711970.27463500X-RAY DIFFRACTION99.6
1.84-1.940.29971890.24593555X-RAY DIFFRACTION99.6
1.94-2.060.26641880.24473505X-RAY DIFFRACTION99.5
2.06-2.220.26151950.22883563X-RAY DIFFRACTION99.1
2.22-2.440.29251740.23243555X-RAY DIFFRACTION99.4
2.44-2.80.30251840.24263558X-RAY DIFFRACTION99.2
2.8-3.520.26251630.21213603X-RAY DIFFRACTION99.2
3.52-32.60.191930.18453656X-RAY DIFFRACTION98.8

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