[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleChanges in the quaternary structure and function of MjHSP16.5 attributable to deletion of the IXI motif and introduction of the substitution, R107G, in the α-crystallin domain.
Journal, issue, pagesPhilos Trans R Soc Lond B Biol Sci, Vol. 368, Issue 1617, Page 20120327, Year 2013
Publish dateMay 5, 2013
AuthorsRoy A Quinlan / Yan Zhang / Andrew Lansbury / Ian Williamson / Ehmke Pohl / Fei Sun /
PubMed AbstractThe archael small heat-shock protein (sHSP), MjHSP16.5, forms a 24-subunit oligomer with octahedral symmetry. Here, we demonstrate that the IXI motif present in the C-terminal domain is necessary for ...The archael small heat-shock protein (sHSP), MjHSP16.5, forms a 24-subunit oligomer with octahedral symmetry. Here, we demonstrate that the IXI motif present in the C-terminal domain is necessary for the oligomerization of MjHSP16.5. Removal increased the in vitro chaperone activity with citrate synthase as the client protein. Less predictable were the effects of the R107G substitution in MjHSP16.5 because of the differences in the oligomerization of metazoan and non-metazoan sHSPs. We present the crystal structure for MjHSP16.5 R107G and compare this with an improved (2.5 Å) crystal structure for wild-type (WT) MjHSP16.5. Although no significant structural differences were found in the crystal, using cryo-electron microscopy, we identified two 24mer species with octahedral symmetry for the WT MjHSP16.5 both at room temperature and at 60°C, all showing two major species with the same diameter of 12.4 nm. Similarly, at room temperature, there are also two kinds of 12.4 nm oligomers for R107G MjHSP16.5, but in the 60°C sample, a larger 24mer species with a diameter of 13.6 nm was observed with significant changes in the fourfold symmetry axis and dimer-dimer interface. This highly conserved arginine, therefore, contributes to the quaternary organization of non-metazoan sHSP oligomers. Potentially, the R107G substitution has functional consequences as R107G MjHSP16.5 was far superior to the WT protein in protecting βL-crystallin against heat-induced aggregation.
External linksPhilos Trans R Soc Lond B Biol Sci / PubMed:23530263 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.85 - 15.0 Å
Structure data

EMDB-2288:
First 3D model of wild type MjHSP16.5 at room temperature by CryoEM.
Method: EM (single particle) / Resolution: 12.0 Å

EMDB-2289:
Second 3D model of wild type MjHSP16.5 at room temperature by CryoEM.
Method: EM (single particle) / Resolution: 12.0 Å

EMDB-2290:
First 3D model of wild type MjHSP16.5 at 60 degree Celsius by CryoEM.
Method: EM (single particle) / Resolution: 14.0 Å

EMDB-2291:
Second 3D model of wild type MjHSP16.5 at 60 degree Celsius by CryoEM.
Method: EM (single particle) / Resolution: 14.0 Å

EMDB-2292:
First 3D model of the MjHSP16.5 mutant R107G at room temperature by CryoEM.
Method: EM (single particle) / Resolution: 10.0 Å

EMDB-2293:
Second 3D model of the MjHSP16.5 mutant R107G at room temperature by CryoEM.
Method: EM (single particle) / Resolution: 10.0 Å

EMDB-2294:
First 3D model of the MjHSP16.5 mutant R107G at 60 degree Celsius by CryoEM.
Method: EM (single particle) / Resolution: 15.0 Å

EMDB-2295:
Second 3D model of the MjHSP16.5 mutant R107G at 60 degree Celsius by CryoEM.
Method: EM (single particle) / Resolution: 15.0 Å

PDB-4i88:
R107G HSP16.5
Method: X-RAY DIFFRACTION / Resolution: 2.85 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • methanocaldococcus jannaschii (archaea)
KeywordsCHAPERONE / alpha-B domain

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more