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- PDB-2b8y: Crystal structure of the interleukin-4 variant T13DF82D -

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Basic information

Entry
Database: PDB / ID: 2b8y
TitleCrystal structure of the interleukin-4 variant T13DF82D
ComponentsInterleukin-4
KeywordsCYTOKINE / Four Helix Bundle
Function / homology
Function and homology information


interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation ...interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of complement-dependent cytotoxicity / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation / neuroinflammatory response / interleukin-4-mediated signaling pathway / positive regulation of isotype switching to IgG isotypes / myeloid dendritic cell differentiation / macrophage activation / positive regulation of interleukin-13 production / positive regulation of amyloid-beta clearance / type 2 immune response / activation of Janus kinase activity / regulation of phosphorylation / positive regulation of MHC class II biosynthetic process / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / positive regulation of macroautophagy / positive regulation of interleukin-10 production / 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 tyrosine phosphorylation of STAT protein / positive regulation of B cell proliferation / cholesterol metabolic process / B cell differentiation / T cell activation / cytokine activity / 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; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKraich, M. / Klein, M. / Patino, E. / Harrer, H. / Sebald, W. / Mueller, T.D.
CitationJournal: Bmc Biol. / Year: 2006
Title: A modular interface of IL-4 allows for scalable affinity without affecting specificity for the IL-4 receptor
Authors: Kraich, M. / Klein, M. / Patino, E. / Harrer, H. / Nickel, J. / Sebald, W. / Mueller, T.D.
History
DepositionOct 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5487
Polymers14,9711
Non-polymers5766
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.032, 91.032, 46.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1115-

HOH

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Components

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


Mass: 14971.145 Da / Num. of mol.: 1 / Mutation: T13D, F82D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P05112
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 52% Ammonium sulfate, 0.1M Sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.8→20.5 Å / Num. all: 18425 / Num. obs: 18359 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HIK

1hik


Resolution: 1.8→14.79 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.983 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 942 5.1 %RANDOM
Rwork0.21639 ---
all0.21768 18359 --
obs0.21768 17414 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→14.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 30 128 1204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211087
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9781465
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02772
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.3503
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.5147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.367
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.528
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2722643
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.19531039
X-RAY DIFFRACTIONr_scbond_it1.6492444
X-RAY DIFFRACTIONr_scangle_it2.5663426
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 70
Rwork0.263 1248
Refinement TLS params.Method: refined / Origin x: 15.072 Å / Origin y: 29.535 Å / Origin z: -14.12 Å
111213212223313233
T0.0112 Å20.0094 Å20.0135 Å2-0.0507 Å2-0.0548 Å2--0.1179 Å2
L2.5848 °2-0.3532 °20.9353 °2-0.8587 °2-0.2766 °2--1.1171 °2
S0.0525 Å °0.1927 Å °-0.0283 Å °-0.1224 Å °0.0413 Å °-0.0325 Å °0.0782 Å °0.162 Å °-0.0938 Å °

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