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- PDB-3l5w: Crystal structure of the complex between IL-13 and C836 FAB -

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Basic information

Entry
Database: PDB / ID: 3l5w
TitleCrystal structure of the complex between IL-13 and C836 FAB
Components
  • C836 HEAVY CHAIN
  • C836 LIGHT CHAIN
  • Interleukin-13
KeywordsIMMUNE SYSTEM / immunoglobulin fold / alpha-helical bundle / Cytokine / Disulfide bond / Glycoprotein / Polymorphism / 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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Human framework adaptation of a mouse anti-human IL-13 antibody.
Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, ...Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, S. / Zhao, Y. / Swanson, R.V. / Almagro, J.C.
History
DepositionDec 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 1.3Nov 27, 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
L: C836 LIGHT CHAIN
H: C836 HEAVY CHAIN
I: Interleukin-13
A: C836 LIGHT CHAIN
B: C836 HEAVY CHAIN
J: Interleukin-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6417
Polymers121,5496
Non-polymers921
Water7,674426
1
L: C836 LIGHT CHAIN
H: C836 HEAVY CHAIN
I: Interleukin-13


Theoretical massNumber of molelcules
Total (without water)60,7743
Polymers60,7743
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: C836 LIGHT CHAIN
B: C836 HEAVY CHAIN
J: Interleukin-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8674
Polymers60,7743
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.620, 65.560, 118.740
Angle α, β, γ (deg.)90.00, 107.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody C836 LIGHT CHAIN


Mass: 23503.090 Da / Num. of mol.: 2
Fragment: CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens
Cell line (production host): Chinese hamster ovary (CHO) cells
Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody C836 HEAVY CHAIN


Mass: 24780.824 Da / Num. of mol.: 2
Fragment: CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens
Cell line (production host): Chinese hamster ovary (CHO) cells
Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Interleukin-13 / IL-13


Mass: 12490.583 Da / Num. of mol.: 2 / Fragment: UNP residues 35-146
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.35 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.1 M HEPES PH 7.5, 20% PEG 3350, 0.2 M SODIUM TARTRATE; CRYO CONDITIONS: MOTHER LIQUOR + 18% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 31, 2008 / Details: VARIMAX HF
RadiationMonochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 76032 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0005refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q9Q

1q9q
PDB Unreleased entry


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.45 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.17 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3812 5 %RANDOM
Rwork0.205 ---
obs0.208 72036 94.7 %-
all-72036 --
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: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.29 Å2
2--0.32 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8073 0 6 426 8505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028275
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9511240
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7551047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03424.61312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92151379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2281525
X-RAY DIFFRACTIONr_chiral_restr0.0970.21281
X-RAY DIFFRACTIONr_gen_planes_refined00.026108
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.23545
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25638
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2550
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.59825383
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.24848489
X-RAY DIFFRACTIONr_scbond_it24.615883337
X-RAY DIFFRACTIONr_scangle_it27.965882751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 264 -
Rwork0.279 5187 -
obs--98.6 %

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