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- PDB-5lqb: Complex structure of human IL2 mutant, Proleukin, with Fab fragme... -

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Basic information

Entry
Database: PDB / ID: 5lqb
TitleComplex structure of human IL2 mutant, Proleukin, with Fab fragment of NARA1 antibody
Components
  • Interleukin-2
  • anti-hIL2 FAB fragment heavy chain
  • anti-hIL2 FAB fragment light chain
KeywordsCYTOKINE / IL2 / Proleukin / NARA1 / anti-IL2
Function / homology
Function and homology information


response to tacrolimus / kappa-type opioid receptor binding / interleukin-2 receptor binding / glycosphingolipid binding / positive regulation of plasma cell differentiation / positive regulation of leukocyte differentiation / 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 ...response to tacrolimus / kappa-type opioid receptor binding / interleukin-2 receptor binding / glycosphingolipid binding / positive regulation of plasma cell differentiation / positive regulation of leukocyte differentiation / 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 / interleukin-2-mediated signaling pathway / positive regulation of leukocyte proliferation / natural killer cell activation / Interleukin-2 signaling / cell surface receptor signaling pathway via STAT / negative regulation of B cell apoptotic process / positive regulation of activated T cell proliferation / kinase activator activity / positive regulation of interleukin-17 production / positive regulation of regulatory T cell differentiation / positive regulation of dendritic spine development / positive regulation of immunoglobulin production / T cell differentiation / positive regulation of B cell proliferation / Interleukin receptor SHC signaling / cell surface receptor signaling pathway via JAK-STAT / cytokine activity / growth factor activity / positive regulation of inflammatory response / phospholipase C-activating G protein-coupled receptor signaling pathway / cell-cell signaling / positive regulation of cell growth / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / RAF/MAP kinase cascade / response to ethanol / adaptive immune response / cell adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / : / 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; / Immunoglobulins / Up-down Bundle ...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; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZou, C. / Wirth, E.
CitationJournal: Sci Transl Med / Year: 2016
Title: Improved cancer immunotherapy by a CD25-mimobody conferring selectivity to human interleukin-2.
Authors: Arenas-Ramirez, N. / Zou, C. / Popp, S. / Zingg, D. / Brannetti, B. / Wirth, E. / Calzascia, T. / Kovarik, J. / Sommer, L. / Zenke, G. / Woytschak, J. / Regnier, C.H. / Katopodis, A. / Boyman, O.
History
DepositionAug 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-2
H: anti-hIL2 FAB fragment heavy chain
L: anti-hIL2 FAB fragment light chain


Theoretical massNumber of molelcules
Total (without water)63,0493
Polymers63,0493
Non-polymers00
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-32 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.757, 36.233, 88.707
Angle α, β, γ (deg.)90.00, 102.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-288-

HOH

21H-503-

HOH

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Components

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


Mass: 15348.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P60568
#2: Antibody anti-hIL2 FAB fragment heavy chain


Mass: 23775.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody anti-hIL2 FAB fragment light chain


Mass: 23925.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 0.2M Sodium Nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→58.74 Å / Num. obs: 39422 / % possible obs: 84.8 % / Redundancy: 3.2 % / Rrim(I) all: 0.079 / Rsym value: 0.066 / Net I/σ(I): 14.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.22 % / Mean I/σ(I) obs: 2.59 / Rsym value: 0.394 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3INK, 3TT1

3ink

3tt1


Resolution: 1.95→58.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.915 / SU B: 17.501 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R Free: 0.219 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29083 1972 5 %RANDOM
Rwork0.18914 ---
obs0.19435 37450 84.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0.46 Å2
2--0.67 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.95→58.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4329 0 0 494 4823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.024442
X-RAY DIFFRACTIONr_bond_other_d0.0040.024071
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9496046
X-RAY DIFFRACTIONr_angle_other_deg1.16239417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.665563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32825.138181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27215720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.91513
X-RAY DIFFRACTIONr_chiral_restr0.1330.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025020
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02981
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.6384.0652258
X-RAY DIFFRACTIONr_mcbond_other7.6384.0642257
X-RAY DIFFRACTIONr_mcangle_it9.1286.1032819
X-RAY DIFFRACTIONr_mcangle_other9.1266.1062820
X-RAY DIFFRACTIONr_scbond_it8.2954.2632184
X-RAY DIFFRACTIONr_scbond_other8.2674.2552182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.3126.2583227
X-RAY DIFFRACTIONr_long_range_B_refined13.27651.3665151
X-RAY DIFFRACTIONr_long_range_B_other12.06550.115030
X-RAY DIFFRACTIONr_rigid_bond_restr4.01138513
X-RAY DIFFRACTIONr_sphericity_free81.6585224
X-RAY DIFFRACTIONr_sphericity_bonded39.00358682
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 166 -
Rwork0.253 3139 -
obs--95.99 %

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