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- PDB-8cgf: Interleukin-4 (wild type) pH 2.4 -

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Basic information

Entry
Database: PDB / ID: 8cgf
TitleInterleukin-4 (wild type) pH 2.4
ComponentsInterleukin-4
KeywordsIMMUNE SYSTEM / Protein / short-chain cytokine / pleiotropic / interleukin / 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 / dendritic cell differentiation / positive regulation of T-helper 2 cell cytokine production ...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 / dendritic cell differentiation / positive regulation of T-helper 2 cell cytokine production / interleukin-4-mediated signaling pathway / neuroinflammatory response / positive regulation of isotype switching to IgG isotypes / positive regulation of interleukin-13 production / macrophage activation / myeloid dendritic cell differentiation / positive regulation of amyloid-beta clearance / regulation of phosphorylation / positive regulation of MHC class II biosynthetic process / negative regulation of cellular response to transforming growth factor beta stimulus / type 2 immune response / 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 / cell surface receptor signaling pathway via JAK-STAT / regulation of immune response / negative regulation of endothelial cell apoptotic process / positive regulation of T cell proliferation / positive regulation of B cell proliferation / B cell differentiation / cholesterol metabolic process / 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 / 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. / Loureiro-Ferreira, N. / Mueller, T. / Sebald, W. / Redfield, C. / Brito, R.M.M.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaUIDB/00313/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/00313/2020 Portugal
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
DepositionFeb 4, 2023Deposition 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 9, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-4


Theoretical massNumber of molelcules
Total (without water)14,9891
Polymers14,9891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
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: 14989.248 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
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
111isotropic32D 1H-13C HSQC
121isotropic32D 1H-15N HSQC
131isotropic33D 1H-13C NOESY
141isotropic33D 1H-15N NOESY
151isotropic33D 1H-15N TOCSY
161isotropic33D (H)CCH-COSY
171isotropic33D HOHAHA-HSQC
181anisotropic22D HSQC IPAP
191isotropic22D HSQC IPAP
1101anisotropic12D HSQC IPAP
1111isotropic12D HSQC IPAP

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-13C; U-15N] Interleukin-4, 95% H2O/5% D2O
Details: 13C-15N uniformly labelled sample of wild type interleukin-4 (IL-4), at pH 2.4, 298K
Label: 13C_15N_IL-4 / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.5 mM / Component: Interleukin-4 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 20 mM NaPi mM / Ionic strength err: 0.1 / Label: 1 / pH: 2.4 / PH err: 0.05 / 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 OxfordOxfordOxford5001
Oxford OxfordOxfordOxford6002
Oxford OxfordOxfordOxford7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH3.6Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH3.6Schwieters, Kuszewski, Tjandra and Clorestructure calculation
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.peak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
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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