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- PDB-8a4f: Human Interleukin-4 mutant - C3T-IL4 -

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Basic information

Entry
Database: PDB / ID: 8a4f
TitleHuman Interleukin-4 mutant - C3T-IL4
ComponentsInterleukin-4
KeywordsCYTOKINE / Interleukin-4 / IL-4 / disulphide mutant / C3T / 4-helix bundle / Backbone dynamics / Molecular dynamics
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 / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsVaz, D.C. / Rodrigues, J.R. / Mueller, T.D. / Sebald, W. / Redfield, C. / Brito, R.M.M.
Funding supportEuropean Union, Portugal, 7items
OrganizationGrant numberCountry
European Regional Development FundCOMPETE Programme (Operational Programme for Competitiveness)European Union
Fundacao para a Ciencia e a TecnologiaREEQ/481/QUI/2006 Portugal
Fundacao para a Ciencia e a TecnologiaRECI/QEQ-QFI/0168/2012 Portugal
European Regional Development FundCENTRO-07-CT62-FEDER-002012European Union
European Regional Development FundRede RNRMNEuropean Union
Fundacao para a Ciencia e a TecnologiaPOCTI/BIO/35685/2000 Portugal
European Communitys Seventh Framework ProgrammeBIO-NMR grant - Bio-NMR Research InfrastructuresEuropean Union
CitationJournal: Proteins / Year: 2024
Title: Lessons on protein structure from interleukin-4: All disulfides are not created equal.
Authors: Vaz, D.C. / Rodrigues, J.R. / Loureiro-Ferreira, N. / Muller, T.D. / Sebald, W. / Redfield, C. / Brito, R.M.M.
History
DepositionJun 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: database_2 / pdbx_entry_details ...database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-4


Theoretical massNumber of molelcules
Total (without water)14,9871
Polymers14,9871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 14987.209 Da / Num. of mol.: 1 / Mutation: C3T
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D 1H-15N NOESY
131isotropic23D 1H-15N TOCSY
141isotropic12D HMQC-J
151anisotropic12D 1H-15N HSQC IPAP
171isotropic12D 1H-15N HSQC IPAP

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-100% 15N] Interleukin-4 mutant, C3T-IL4, 90% H2O/10% D2O
Details: 1.5 mM 15N C3T-IL-4 sample, in 25 mM NaCD3COO/CD3COOD, 9:1 H2O/D2O, 0.05 % NaN3, pH 5.0, 298 K
Label: 15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: Interleukin-4 mutant, C3T-IL4 / Isotopic labeling: [U-100% 15N]
Sample conditionsDetails: 15N C3T-IL-4 sample, in 25 mM NaCD3COO/CD3COOD, 9:1 H2O/D2O, 0.05 % NaN3, pH 5.0, 298 K
Ionic strength: 25 mM / Ionic strength err: 0.1 / Label: conditions_1 / pH: 5 / PH err: 0.01 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Oxford instruments home builtOxford instrumentshome built6001
Oxford instruments home builtOxford instrumentshome built7502
Oxford instruments home builtOxford instrumentshome built5003

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.peak picking
FelixAccelrys Software Inc.chemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 2

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