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- PDB-4i77: Lebrikizumab Fab bound to IL-13 -

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Basic information

Entry
Database: PDB / ID: 4i77
TitleLebrikizumab Fab bound to IL-13
Components
  • Interleukin-13
  • Lebrikizumab heavy chain
  • Lebrikizumab light chain
KeywordsIMMUNE SYSTEM/CYTOKINE / immunoglobulin / immune system recognition / IMMUNE SYSTEM-CYTOKINE complex
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEigenbrot, C. / Ultsch, M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Basis of Signaling Blockade by Anti-IL-13 Antibody Lebrikizumab.
Authors: Ultsch, M. / Bevers, J. / Nakamura, G. / Vandlen, R. / Kelley, R.F. / Wu, L.C. / Eigenbrot, C.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Lebrikizumab heavy chain
L: Lebrikizumab light chain
Z: Interleukin-13


Theoretical massNumber of molelcules
Total (without water)59,6503
Polymers59,6503
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-36 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.722, 64.772, 117.101
Angle α, β, γ (deg.)90.00, 106.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Lebrikizumab heavy chain


Mass: 23434.465 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Lebrikizumab light chain


Mass: 23856.365 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Interleukin-13 / IL-13


Mass: 12359.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13, NC30 / Production host: Escherichia coli (E. coli) / References: UniProt: P35225
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% w/v PEG1000, 0.05 M sodium malonate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→29.12 Å / Num. all: 46433 / Num. obs: 46431 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.39 Å2 / Rsym value: 0.065 / Net I/σ(I): 18
Reflection shellHighest resolution: 1.9 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.517 / % possible all: 92.1

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
BUSTER2.11.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVC

1fvc


Resolution: 1.9→29.12 Å / Cor.coef. Fo:Fc: 0.9575 / Cor.coef. Fo:Fc free: 0.9335 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.13 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 944 2.03 %RANDOM
Rwork0.1791 ---
obs0.1798 46431 97.58 %-
all-46433 --
Displacement parametersBiso mean: 49.01 Å2
Baniso -1Baniso -2Baniso -3
1--5.0878 Å20 Å24.5221 Å2
2---1.4082 Å20 Å2
3---6.4961 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 0 378 4446
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014180HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.175687HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1423SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes608HARMONIC5
X-RAY DIFFRACTIONt_it4180HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion18.61
X-RAY DIFFRACTIONt_chiral_improper_torsion565SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5126SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2014 61 2.12 %
Rwork0.2232 2817 -
all0.2227 2878 -
obs--97.58 %
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)
11.1929-0.0851-0.86240.71950.7673.8050.0525-0.21440.10190.25750.2406-0.22030.26530.5046-0.2931-0.02250.1421-0.05080.005-0.1027-0.081218.484919.9181-28.1736
22.62850.46710.51512.65910.38061.6342-0.0234-0.00840.11540.0812-0.03080.2879-0.0018-0.04480.0542-0.06120.03640.0303-0.0774-0.0203-0.0082-4.557427.4737-48.5464
32.2678-0.37140.35990.72230.12473.19770.1465-0.2169-0.10060.3222-0.00460.09970.6643-0.4176-0.14190.2736-0.0833-0.0275-0.10920.0247-0.20980.99313.8838-16.0603
41.59380.74940.41681.60041.29012.87550.0655-0.080.01820.0868-0.09830.14930.079-0.27530.0328-0.08070.01410.0123-0.0688-0.0054-0.0497-13.367415.2233-51.2911
54.2339-0.91932.20212.3224-1.71458.16410.0687-0.3416-0.13130.09760.1852-0.3570.00310.4512-0.254-0.08520.1881-0.08130.2993-0.1039-0.369126.60421.62641.3207
6-0.96472.09011.36260.26610.75762.1476-0.0106-0.0439-0.00350.00780.026-0.01260.0324-0.0061-0.01540.2913-0.10850.00780.2621-0.1722-0.301217.69229.492611.5563
70.0818-1.0266-1.32921.27330.0268.23370.0133-0.3277-0.0610.60730.3431-0.14150.49540.4719-0.35640.01450.1881-0.06510.1356-0.1039-0.349416.061922.3143-0.2564
8-0.07390.2914-0.044500.87171.197-0.0018-0.06140.04850.0629-0.0094-0.037-0.02910.04050.01130.18310.0215-0.00960.115-0.152-0.064812.053834.66523.2766
9-1.4632-2.37932.16210.56631.76892.59420.0793-0.127-0.3264-0.05050.0037-0.0928-0.00570.0559-0.083-0.08680.0466-0.0230.2683-0.1447-0.332426.357625.90318.3891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{H|1 - 119}H1 - 119
2X-RAY DIFFRACTION2{H|120 - 214}H120 - 214
3X-RAY DIFFRACTION3{L|1 - 107}L1 - 107
4X-RAY DIFFRACTION4{L|108 - 214}L108 - 214
5X-RAY DIFFRACTION5{Z|8 - 35}Z8 - 35
6X-RAY DIFFRACTION6{Z|36 - 43}Z36 - 43
7X-RAY DIFFRACTION7{Z|44 - 75}Z44 - 75
8X-RAY DIFFRACTION8{Z|76 - 88}Z76 - 88
9X-RAY DIFFRACTION9{Z|89 - 108}Z89 - 108

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