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- PDB-3g6d: Crystal structure of the complex between CNTO607 Fab and IL-13 -

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Basic information

Entry
Database: PDB / ID: 3g6d
TitleCrystal structure of the complex between CNTO607 Fab and IL-13
Components
  • CNTO607 Fab Heavy chain
  • CNTO607 Fab Light chain
  • Interleukin-13
KeywordsIMMUNE SYSTEM / IL-13 / antibody / complex / epitope / Cytokine / Glycoprotein / Secreted / MONOCLONAL ANTIBODY
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 / interleukin-13-mediated signaling pathway / regulation of proton transport / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / positive regulation of mast cell degranulation ...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 / interleukin-13-mediated signaling pathway / regulation of proton transport / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / positive regulation of mast cell degranulation / macrophage activation / response to selenium ion / response to nematode / positive regulation of macrophage activation / positive regulation of immunoglobulin production / positive regulation of interleukin-10 production / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of release of sequestered calcium ion into cytosol / cytokine activity / positive regulation of protein secretion / response to nicotine / cellular response to mechanical stimulus / microglial cell activation / negative regulation of inflammatory response / positive regulation of cold-induced thermogenesis / response to ethanol / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / immune response / inflammatory response / external side of plasma membrane / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Epitope mapping of anti-interleukin-13 neutralizing antibody CNTO607.
Authors: Teplyakov, A. / Obmolova, G. / Wu, S.J. / Luo, J. / Kang, J. / O'Neil, K. / Gilliland, G.L.
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: CNTO607 Fab Light chain
H: CNTO607 Fab Heavy chain
A: Interleukin-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6684
Polymers59,5723
Non-polymers961
Water00
1
A: Interleukin-13

L: CNTO607 Fab Light chain
H: CNTO607 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6684
Polymers59,5723
Non-polymers961
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_554-x,y+1/2,-z-1/21
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-31.9 kcal/mol
Surface area24210 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-27.3 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.540, 68.030, 182.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody CNTO607 Fab Light chain


Mass: 22619.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Human Embryonic Kidney 293 cells / Cell line (production host): HEK 293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
#2: Antibody CNTO607 Fab Heavy chain


Mass: 24461.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Human Embryonic Kidney 293 cells / Cell line (production host): HEK 293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
#3: Protein Interleukin-13 / IL-13


Mass: 12490.583 Da / Num. of mol.: 1 / Fragment: UNP residues 21-132
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY
Sequence detailsFAB WAS OBTAINED BY PAPAIN CLEAVAGE OF ANTIBODY.

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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: 3.5 Å3/Da / Density % sol: 65 %
Description: The overall R-merge is very high because of very weak diffraction.
Crystal growTemperature: 293 K / pH: 4.5
Details: 0.1 M Sodium acetate pH 4.5, 4.9 M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 22, 2006 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→63 Å / Num. obs: 13028 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 6.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.6 / % possible all: 88.2

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Processing

Software
NameVersionClassification
d*TREK9.6Ldata scaling
PHASERphasing
REFMAC5.2.0005refinement
d*TREK9.6Ldata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3G6A, 1IJZ

3g6a

1ijz


Resolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.823 / SU B: 28.326 / SU ML: 0.443 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.647 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26342 501 3.9 %RANDOM
Rwork0.213 ---
obs0.213 12362 100 %-
all-16206 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--2.76 Å20 Å2
3----1.58 Å2
Refine analyzeLuzzati coordinate error free: 0.457 Å
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 5 0 4059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224155
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9515670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7045536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71624.78159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.07915647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.41514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2645
X-RAY DIFFRACTIONr_gen_planes_refined00.023132
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21865
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22826
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.38722735
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.75204332
X-RAY DIFFRACTIONr_scbond_it20.351401635
X-RAY DIFFRACTIONr_scangle_it26.417991338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 32 -
Rwork0.28 823 -
all0.28 --
obs--88.2 %

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