[English] 日本語
Yorodumi
- PDB-8a4f: Human Interleukin-4 mutant - C3T-IL4 -

+
Open data


ID or keywords:

Loading...

-
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 / 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 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
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

-
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

+
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://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