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- PDB-5l6y: il13 in complex with tralokinumab -

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Basic information

Entry
Database: PDB / ID: 5l6y
Titleil13 in complex with tralokinumab
Components
  • Interleukin-13
  • tralokinumab FAb digest VH
  • tralokiumab FAb digest VL
KeywordsIMMUNE SYSTEM / IL13 antibody tralokinumab asthma / IL13
Function / homology
Function and homology information


interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / regulation of proton transport / positive regulation of connective tissue growth factor production / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / macrophage activation ...interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / regulation of proton transport / positive regulation of connective tissue growth factor production / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / macrophage activation / positive regulation of mast cell degranulation / positive regulation of macrophage activation / positive regulation of immunoglobulin production / cellular response to cytokine stimulus / positive regulation of interleukin-10 production / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of release of sequestered calcium ion into cytosol / cytokine activity / positive regulation of protein secretion / positive regulation of smooth muscle cell proliferation / microglial cell activation / response to nicotine / negative regulation of inflammatory response / cellular response to mechanical stimulus / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / response to ethanol / response to lipopolysaccharide / inflammatory response / immune response / external side of plasma membrane / positive regulation of gene expression / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Interleukin-13 / Interleukin-13 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins ...Interleukin-13 / Interleukin-13 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / 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
FORMIC ACID / Interleukin-13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsBreed, J.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Characterisation Reveals Mechanism of IL-13-Neutralising Monoclonal Antibody Tralokinumab as Inhibition of Binding to IL-13R alpha 1 and IL-13R alpha 2.
Authors: Popovic, B. / Breed, J. / Rees, D.G. / Gardener, M.J. / Vinall, L.M. / Kemp, B. / Spooner, J. / Keen, J. / Minter, R. / Uddin, F. / Colice, G. / Wilkinson, T. / Vaughan, T. / May, R.D.
History
DepositionJun 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Interleukin-13
H: tralokinumab FAb digest VH
L: tralokiumab FAb digest VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,06718
Polymers60,3773
Non-polymers69015
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-36 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.998, 53.195, 62.050
Angle α, β, γ (deg.)107.91, 101.42, 96.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Interleukin-13 / IL-13


Mass: 12359.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IL13 R&D Systems (Recombinant Human IL-13 cat no:213-ILB/CF)
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13, NC30 / Production host: Escherichia coli (E. coli) / References: UniProt: P35225
#2: Antibody tralokinumab FAb digest VH


Mass: 25333.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody tralokiumab FAb digest VL


Mass: 22684.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9749 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9749 Å / Relative weight: 1
ReflectionResolution: 1.99→49.65 Å / Num. obs: 39821 / % possible obs: 97.7 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.93 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.7
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 93.4

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 1.99→49.65 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.882 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1763 4.98 %RANDOM
Rwork0.189 ---
obs0.19 35416 97.8 %-
Displacement parametersBiso mean: 25.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.2556 Å2-8.8266 Å2-2.1301 Å2
2---6.5742 Å2-5.621 Å2
3---4.3187 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.99→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 45 210 4208
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0224104HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185592HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1284SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes606HARMONIC5
X-RAY DIFFRACTIONt_it4104HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.04
X-RAY DIFFRACTIONt_other_torsion14.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion557SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4669SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.233 -3.82 %
Rwork0.213 1460 -
all0.213 1518 -
obs--87.49 %
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)
11.3377-0.7499-0.25150.99960.66091.3035-0.02210.0140.141-0.0304-0.0992-0.0976-0.0528-0.10550.12120.00250.07070.0383-0.05710.00610.029-21.823626.3244-13.4211
20.8022-0.30580.99350.4419-0.68691.39190.09640.01570.0235-0.0814-0.0690.02290.1547-0.013-0.0274-0.02370.01970.0309-0.0016-0.0445-0.04667.4588-10.9978-1.7492
30.8143-0.35680.49960.1357-0.32820.302-0.017-0.16750.0913-0.0020.0386-0.045-0.0164-0.05-0.0216-0.0140.01390.00720.0104-0.03880.00571.56520.12088.3157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ C|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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