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- PDB-2b8z: Crystal structure of the interleukin-4 variant R85A -

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Basic information

Entry
Database: PDB / ID: 2b8z
TitleCrystal structure of the interleukin-4 variant R85A
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 / 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 amyloid-beta clearance / regulation of phosphorylation / type 2 immune response / activation of Janus kinase activity / 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 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 / T cell activation / cholesterol metabolic process / B cell differentiation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2875
Polymers14,9031
Non-polymers3844
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.190, 91.190, 45.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 14903.133 Da / Num. of mol.: 1 / Mutation: R85A
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 61.47 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 21, 2004 / Details: Mirror
RadiationMonochromator: Rigaku VariMax Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→32.3 Å / Num. all: 8464 / Num. obs: 8375 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HIK

1hik


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.394 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26368 334 4.8 %RANDOM
Rwork0.21091 ---
all0.21352 7065 --
obs0.21352 6654 98.95 %-
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: 34.463 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 20 104 1166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9671457
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135128
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_restr0.0880.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02771
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.3544
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2590.5131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.369
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.521
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7051.5643
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36721040
X-RAY DIFFRACTIONr_scbond_it2.0653439
X-RAY DIFFRACTIONr_scangle_it3.5984.5417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 28
Rwork0.224 472
Refinement TLS params.Method: refined / Origin x: 14.9718 Å / Origin y: 29.4397 Å / Origin z: -13.9843 Å
111213212223313233
T0.0327 Å2-0.005 Å20.0327 Å2-0.0051 Å2-0.004 Å2--0.033 Å2
L4.3182 °2-1.152 °21.7396 °2-0.6206 °20.019 °2--1.5456 °2
S0.0649 Å °0.248 Å °0.0595 Å °-0.1804 Å °-0.0087 Å °-0.0868 Å °-0.0732 Å °0.1799 Å °-0.0562 Å °

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