[English] 日本語
Yorodumi
- PDB-4aka: IPSE alpha-1, an IgE-binding crystallin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aka
TitleIPSE alpha-1, an IgE-binding crystallin
ComponentsIL-4-INDUCING PROTEIN
KeywordsIMMUNE SYSTEM / SCHISTOSOMA MANSONI / IMMUNOGLOBULIN BINDING
Function / homologyInterleukin-4 inducing immunoglobulin-binding domain / Interleukin-4 inducing immunoglobulin-binding domain / Crystallins / Gamma-B Crystallin; domain 1 / Gamma-crystallin-like / Sandwich / Mainly Beta / IL-4-inducing protein
Function and homology information
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodSOLUTION NMR / CYANA
AuthorsMeyer, N.H. / Mayerhofer, H. / Tripsianes, K. / Barths, D. / Blindow, S. / Bade, S. / Madl, T. / Frey, A. / Haas, H. / Mueller-Dieckmann, J. ...Meyer, N.H. / Mayerhofer, H. / Tripsianes, K. / Barths, D. / Blindow, S. / Bade, S. / Madl, T. / Frey, A. / Haas, H. / Mueller-Dieckmann, J. / Sattler, M. / Scharmm, G.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: A Crystallin Fold in the Interleukin-4-Inducing Principle of Schistosoma Mansoni Eggs (Ipse/Alpha-1) Mediates Ige Binding for Antigen-Independent Basophil Activation
Authors: Meyer, N.H. / Mayerhofer, H. / Tripsianes, K. / Barths, D. / Blindow, S. / Bade, S. / Madl, T. / Frey, A. / Haas, H. / Mueller-Dieckmann, J. / Sattler, M. / Scharmm, G.
#1: Journal: Biomol.NMR Assign. / Year: 2011
Title: 1H, 13C and 15N Chemical Shift Assignments of Ipsedeltanls
Authors: Meyer, N.H. / Schramm, G. / Sattler, M.
History
DepositionFeb 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IL-4-INDUCING PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,9811
Polymers11,9811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

-
Components

#1: Protein IL-4-INDUCING PROTEIN / INTERLEUKIN-4-INDUCING PROTEIN / IPSE ALPHA-1


Mass: 11981.478 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PPROEXHTB IPSEDNLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q869D4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED IPSEDELTANLS

-
Sample preparation

DetailsContents: 10% D2O/ 90% H2O
Sample conditionsIonic strength: 200 mM / pH: 7.2 / Pressure: 1.0 atm / Temperature: 298.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE7502

-
Processing

NMR software
NameVersionDeveloperClassification
CNS, ARIAARIAJP.LINGE,MA.WILLIAMS,CA.SPRONK,AM.BONVIN,M.refinement
NMRPipestructure solution
Sparkystructure solution
CYANAstructure solution
ARIAstructure solution
RefinementMethod: CYANA / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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