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- PDB-7dr4: Complex of anti-human IL-2 antibody and human IL-2 -

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Basic information

Entry
Database: PDB / ID: 7dr4
TitleComplex of anti-human IL-2 antibody and human IL-2
Components
  • Interleukin-2
  • anti-human IL-2 antibody, mouse Ig G, heavy chain
  • anti-human IL-2 antibody, mouse Ig G, kappa chain
KeywordsIMMUNE SYSTEM / Complex / human IL-2 / antibody / Tcell / PROTEIN BINDING
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 / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...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 / glycosphingolipid binding / positive regulation of plasma cell differentiation / 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 / cell surface receptor signaling pathway via STAT / Interleukin-2 signaling / kinase activator activity / natural killer cell activation / 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 / carbohydrate binding / RAF/MAP kinase cascade / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsKim, M.S. / Kim, J.E.
CitationJournal: Oncoimmunology / Year: 2021
Title: Crystal structure of human interleukin-2 in complex with TCB2, a new antibody-drug candidate with antitumor activity.
Authors: Kim, J. / Lee, J.Y. / Park, S.Y. / Lee, Y.J. / Kim, M.S.
History
DepositionDec 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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
H: anti-human IL-2 antibody, mouse Ig G, heavy chain
L: anti-human IL-2 antibody, mouse Ig G, kappa chain
A: anti-human IL-2 antibody, mouse Ig G, heavy chain
B: anti-human IL-2 antibody, mouse Ig G, kappa chain
C: anti-human IL-2 antibody, mouse Ig G, heavy chain
D: anti-human IL-2 antibody, mouse Ig G, kappa chain
E: anti-human IL-2 antibody, mouse Ig G, heavy chain
F: anti-human IL-2 antibody, mouse Ig G, kappa chain
G: Interleukin-2
I: Interleukin-2
J: Interleukin-2
K: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)252,25212
Polymers252,25212
Non-polymers00
Water7,602422
1
H: anti-human IL-2 antibody, mouse Ig G, heavy chain
L: anti-human IL-2 antibody, mouse Ig G, kappa chain
K: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)63,0633
Polymers63,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: anti-human IL-2 antibody, mouse Ig G, heavy chain
B: anti-human IL-2 antibody, mouse Ig G, kappa chain
J: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)63,0633
Polymers63,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: anti-human IL-2 antibody, mouse Ig G, heavy chain
D: anti-human IL-2 antibody, mouse Ig G, kappa chain
G: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)63,0633
Polymers63,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: anti-human IL-2 antibody, mouse Ig G, heavy chain
F: anti-human IL-2 antibody, mouse Ig G, kappa chain
I: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)63,0633
Polymers63,0633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.334, 72.261, 210.930
Angle α, β, γ (deg.)90.000, 92.711, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody
anti-human IL-2 antibody, mouse Ig G, heavy chain


Mass: 23880.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
anti-human IL-2 antibody, mouse Ig G, kappa chain


Mass: 23746.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein
Interleukin-2 / IL-2 / T-cell growth factor / TCGF


Mass: 15435.979 Da / Num. of mol.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M NH4NO3, pH4.8, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.49→48.25 Å / Num. obs: 80414 / % possible obs: 96.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 34.01 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.083 / Rrim(I) all: 0.179 / Net I/σ(I): 1.34
Reflection shellResolution: 2.5→2.5 Å / Num. unique obs: 5025 / CC1/2: 0.442

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LQB

5lqb


Resolution: 2.49→29.79 Å / SU ML: 0.3544 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 1994 2.48 %
Rwork0.1948 78382 -
obs0.1964 80376 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.41 Å2
Refinement stepCycle: LAST / Resolution: 2.49→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16907 0 0 422 17329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008217290
X-RAY DIFFRACTIONf_angle_d1.013923495
X-RAY DIFFRACTIONf_chiral_restr0.05512699
X-RAY DIFFRACTIONf_plane_restr0.0062969
X-RAY DIFFRACTIONf_dihedral_angle_d19.94876299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.35761310.26275025X-RAY DIFFRACTION87.38
2.55-2.620.27481310.24735414X-RAY DIFFRACTION93.38
2.62-2.70.32761380.245438X-RAY DIFFRACTION94.05
2.7-2.790.29411410.23215427X-RAY DIFFRACTION93.22
2.79-2.890.31891380.22195461X-RAY DIFFRACTION93.91
2.89-30.32091380.21995624X-RAY DIFFRACTION96.66
3-3.140.26681470.22185611X-RAY DIFFRACTION96.97
3.14-3.30.29041470.20335701X-RAY DIFFRACTION97.76
3.3-3.510.30951460.19695692X-RAY DIFFRACTION98.12
3.51-3.780.23161430.18735723X-RAY DIFFRACTION97.49
3.78-4.160.21241480.16185795X-RAY DIFFRACTION99.27
4.16-4.760.2051490.14325769X-RAY DIFFRACTION98.83
4.76-5.990.20341470.16815805X-RAY DIFFRACTION97.98
5.99-29.790.25081500.21275897X-RAY DIFFRACTION97.69

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