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- PDB-1hzi: INTERLEUKIN-4 MUTANT E9A -

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Basic information

Entry
Database: PDB / ID: 1hzi
TitleINTERLEUKIN-4 MUTANT E9A
ComponentsINTERLEUKIN-4
KeywordsCYTOKINE / IL-4 / 4-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 / Interleukin-18 signaling / regulation of isotype switching / 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 / Interleukin-18 signaling / regulation of isotype switching / 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-mediated signaling pathway / neuroinflammatory response / positive regulation of isotype switching to IgG isotypes / positive regulation of interleukin-13 production / macrophage activation / positive regulation of amyloid-beta clearance / myeloid dendritic cell differentiation / positive regulation of MHC class II biosynthetic process / type 2 immune response / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / negative regulation of osteoclast differentiation / positive regulation of ATP biosynthetic process / positive regulation of interleukin-10 production / positive regulation of macroautophagy / negative regulation of tumor necrosis factor production / cell surface receptor signaling pathway via JAK-STAT / regulation of immune response / negative regulation of endothelial cell apoptotic process / cholesterol metabolic process / positive regulation of B cell proliferation / positive regulation of T cell proliferation / T cell activation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of receptor-mediated endocytosis / negative regulation of inflammatory response / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / immune response / positive regulation of cell migration / 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: 2.05 Å
AuthorsHulsmeyer, M. / Scheufler, C. / Dreyer, M.K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of interleukin 4 mutant E9A suggests polar steering in receptor-complex formation.
Authors: Hulsmeyer, M. / Scheufler, C. / Dreyer, M.K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: A MIXED-CHARGE PAIR IN HUMAN INTERLEUKIN 4 DOMINATES HIGH-AFFINITY INTERACTION WITH THE RECEPTOR A CHAIN
Authors: Wang, Y. / Shen, B.-J. / Sebald, W.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal Structure of the Interleukin-4/Receptor a chain complex reveals a mosaic binding interface
Authors: Hage, T. / Sebald, W. / Reinemer, P.
History
DepositionJan 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 9, 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

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4126
Polymers14,9311
Non-polymers4805
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.050, 91.050, 45.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer.

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Components

#1: Protein INTERLEUKIN-4 / IL-4


Mass: 14931.213 Da / Num. of mol.: 1 / Mutation: E9A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05112
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.15 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: ammonium sulfate, sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate1reservoir
263 %satammonium sulfate1reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 11, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 12421 / Num. obs: 12421 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 34.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 7.7 / Num. unique all: 795 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99.2 % / Num. measured all: 61298 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 98.8 % / Num. unique obs: 795 / Num. measured obs: 4531

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RCB

1rcb


Resolution: 2.05→19.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1148676.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 886 7.1 %RANDOM
Rwork0.225 ---
obs0.225 12421 99.3 %-
all-12421 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.42 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 25 145 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.782.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 153 7.7 %
Rwork0.252 1842 -
obs-1842 98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / % reflection Rfree: 7.7 % / Rfactor Rwork: 0.252

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