[English] 日本語
Yorodumi
- PDB-8cgf: Interleukin-4 (wild type) pH 2.4 -

+
Open data


ID or keywords:

Loading...

-
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


positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling ...positive regulation of eosinophil chemotaxis / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / B cell costimulation / negative regulation of complement-dependent cytotoxicity / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / negative regulation of T-helper 17 cell differentiation / dendritic cell differentiation / positive regulation of T-helper 2 cell cytokine production / 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 mast cell degranulation / regulation of phosphorylation / positive regulation of mononuclear cell migration / positive regulation of amyloid-beta clearance / type 2 immune response / activation of Janus kinase activity / positive regulation of MHC class II biosynthetic process / T-helper 2 cell differentiation / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of myoblast fusion / positive regulation of ATP biosynthetic process / negative regulation of osteoclast differentiation / negative regulation of acute inflammatory response / 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 / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of defense response to virus by host / T cell activation / cholesterol metabolic process / B cell differentiation / innate immune response in mucosa / cytokine activity / negative regulation of extrinsic apoptotic signaling pathway / microglial cell activation / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Oxford OxfordOxfordOxford5001
Oxford OxfordOxfordOxford6002
Oxford OxfordOxfordOxford7503

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more