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- PDB-5fhx: CRYSTAL STRUCTURE OF CODV IN COMPLEX WITH IL4 AT 2.55 Ang. RESOLUTION. -

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Basic information

Entry
Database: PDB / ID: 5fhx
TitleCRYSTAL STRUCTURE OF CODV IN COMPLEX WITH IL4 AT 2.55 Ang. RESOLUTION.
Components
  • Antibody fragment light chain
  • Interleukin-4
  • antibody fragment heavy-chain
KeywordsIMMUNE SYSTEM / cross-over dual variable immunoglobulin multifunctional biotherapeutic drug / CODV
Function / homology
Function and homology information


positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling ...positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / negative regulation of T-helper 17 cell differentiation / dendritic cell differentiation / positive regulation of T-helper 2 cell cytokine production / positive regulation of isotype switching to IgG isotypes / neuroinflammatory response / interleukin-4-mediated signaling pathway / macrophage activation / positive regulation of interleukin-13 production / myeloid dendritic cell differentiation / positive regulation of mast cell degranulation / regulation of phosphorylation / positive regulation of mononuclear cell migration / positive regulation of amyloid-beta clearance / type 2 immune response / activation of Janus kinase activity / positive regulation of MHC class II biosynthetic process / T-helper 2 cell differentiation / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of myoblast fusion / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / negative regulation of acute inflammatory response / positive regulation of interleukin-10 production / positive regulation of macroautophagy / negative regulation of tumor necrosis factor production / regulation of immune response / negative regulation of endothelial cell apoptotic process / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of defense response to virus by host / T cell activation / cholesterol metabolic process / B cell differentiation / innate immune response in mucosa / cytokine activity / negative regulation of extrinsic apoptotic signaling pathway / microglial cell activation / growth factor activity / negative regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of cell migration / immune response / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-4 / Interleukin 4 / 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-4 / Interleukin 4 / 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
PHOSPHATE ION / Interleukin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsVallee, F. / Dupuy, A. / Rak, A.
CitationJournal: Mabs / Year: 2016
Title: CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications.
Authors: Steinmetz, A. / Vallee, F. / Beil, C. / Lange, C. / Baurin, N. / Beninga, J. / Capdevila, C. / Corvey, C. / Dupuy, A. / Ferrari, P. / Rak, A. / Wonerow, P. / Kruip, J. / Mikol, V. / Rao, E.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-4
H: antibody fragment heavy-chain
L: Antibody fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0285
Polymers87,8383
Non-polymers1902
Water2,306128
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-56 kcal/mol
Surface area37280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.210, 73.330, 91.400
Angle α, β, γ (deg.)90.00, 112.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interleukin-4 / IL-4 / B-cell stimulatory factor 1 / BSF-1 / Binetrakin / Lymphocyte stimulatory factor 1 / Pitrakinra


Mass: 14390.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4 / Production host: Escherichia coli (E. coli) / References: UniProt: P05112
#2: Antibody antibody fragment heavy-chain


Mass: 37281.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Antibody fragment light chain


Mass: 36166.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: PEG 3350 20%, K-Acetate 0.20M / PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.55→23.15 Å / Num. obs: 30823 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 58.53 Å2 / Rsym value: 0.115 / Net I/σ(I): 7.6
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.1 % / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→23.15 Å / Cor.coef. Fo:Fc: 0.9165 / Cor.coef. Fo:Fc free: 0.8779 / SU R Cruickshank DPI: 0.486 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.454 / SU Rfree Blow DPI: 0.277 / SU Rfree Cruickshank DPI: 0.285
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1545 5.01 %RANDOM
Rwork0.1839 ---
obs0.1872 30823 99.86 %-
Displacement parametersBiso mean: 61.11 Å2
Baniso -1Baniso -2Baniso -3
1--19.5531 Å20 Å2-11.573 Å2
2--13.4662 Å20 Å2
3---6.087 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.55→23.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6117 0 10 128 6255
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016265HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.238510HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2112SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes138HARMONIC2
X-RAY DIFFRACTIONt_gen_planes908HARMONIC5
X-RAY DIFFRACTIONt_it6265HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion20.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion838SEMIHARMONIC5
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_contact6816SEMIHARMONIC4
LS refinement shellResolution: 2.55→2.64 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2754 151 5.06 %
Rwork0.2145 2831 -
all0.2178 2982 -
obs--99.86 %

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