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- PDB-4ps4: Crystal structure of the complex between IL-13 and M1295 FAB -

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Basic information

Entry
Database: PDB / ID: 4ps4
TitleCrystal structure of the complex between IL-13 and M1295 FAB
Components
  • Interleukin-13
  • M1295 HEAVY CHAIN
  • M1295 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / ALPHA-HELICAL BUNDLE / CYTOKINE / DISULFIDE BOND / 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 / microglial cell activation / cellular response to mechanical stimulus / 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 / DIFFERENCE FOURIER / Resolution: 2.8 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
DepositionMar 6, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMar 19, 2014ID: 3L5Y
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Sep 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
Revision 2.2Oct 9, 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: M1295 LIGHT CHAIN
H: M1295 HEAVY CHAIN
A: Interleukin-13


Theoretical massNumber of molelcules
Total (without water)60,3933
Polymers60,3933
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.210, 72.160, 113.820
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 M1295 LIGHT CHAIN


Mass: 23358.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo Sapiens (human)
#2: Antibody M1295 HEAVY CHAIN


Mass: 24543.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo Sapiens (human)
#3: Protein Interleukin-13 / IL-13


Mass: 12490.583 Da / Num. of mol.: 1 / 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
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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M SODIUM ACETATE PH 4.5, 25% PEG 8K, 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 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 7, 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: 2.8→30 Å / Num. all: 12722 / Num. obs: 12722 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.8 / % possible all: 62.5

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Processing

Software
NameClassification
CrystalCleardata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 3L5X

3l5x


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.852 / SU B: 18.934 / SU ML: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.45 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27096 622 4.9 %RANDOM
Rwork0.21111 ---
all0.21397 12011 --
obs0.21397 12011 96.3 %-
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: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å2-0 Å20 Å2
2---3.06 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 0 0 3925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024027
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.9675483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2615512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08824.247146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01915671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1861515
X-RAY DIFFRACTIONr_chiral_restr0.0630.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212957
X-RAY DIFFRACTIONr_mcbond_it2.5467.4522051
X-RAY DIFFRACTIONr_mcangle_it4.316.7232556
X-RAY DIFFRACTIONr_scbond_it2.5297.3931976
X-RAY DIFFRACTIONr_long_range_B_refined6.8899.9995684
LS refinement shellResolution: 2.817→2.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 27 -
Rwork0.316 532 -
obs--61.2 %

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