[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

TitleNewly folded substrates inside the molecular cage of the HtrA chaperone DegQ.
Journal, issue, pagesNat Struct Mol Biol, Vol. 19, Issue 2, Page 152-157, Year 2012
Publish dateJan 15, 2012
AuthorsHélène Malet / Flavia Canellas / Justyna Sawa / Jun Yan / Konstantinos Thalassinos / Michael Ehrmann / Tim Clausen / Helen R Saibil /
PubMed AbstractThe HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA ...The HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA proteins are well characterized, their chaperone activity remains poorly understood. Here we describe cryo-EM structures of Escherichia coli DegQ in its 12- and 24-mer states in complex with model substrates, providing a structural model of HtrA chaperone action. Up to six lysozyme substrates bind inside the DegQ 12-mer cage and are visualized in a close-to-native state. An asymmetric reconstruction reveals the binding of a well-ordered lysozyme to four DegQ protomers. DegQ PDZ domains are located adjacent to substrate density and their presence is required for chaperone activity. The substrate-interacting regions appear conserved in 12- and 24-mer cages, suggesting a common mechanism of chaperone function.
External linksNat Struct Mol Biol / PubMed:22245966 / PubMed Central
MethodsEM (single particle)
Resolution7.5 - 28 Å
Structure data

1981

4a8a

EMDB-1981, PDB-4a8a:
Asymmetric cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozyme
Method: EM (single particle) / Resolution: 14.2 Å

1982

4a8b

EMDB-1982, PDB-4a8b:
Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozymes
Method: EM (single particle) / Resolution: 13.0 Å

1983

4a8c

EMDB-1983, PDB-4a8c:
Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide
Method: EM (single particle) / Resolution: 7.5 Å

1984

4a9g

EMDB-1984, PDB-4a9g:
Symmetrized cryo-EM reconstruction of E. coli DegQ 24-mer in complex with beta-casein
Method: EM (single particle) / Resolution: 7.5 Å

PDB-4a8d:
DegP dodecamer with bound OMP
Method: ELECTRON MICROSCOPY / Resolution: 28 Å

Source
  • escherichia coli (E. coli)
  • gallus gallus (chicken)
  • synthetic construct (others)
  • Bos taurus (cattle)
KeywordsHYDROLASE/HYDROLASE / HYDROLASE-HYDROLASE COMPLEX / CHAPERONE / HYDROLASE / HYDROLASE/TRANSPORT PROTEIN / HYDROLASE-TRANSPORT PROTEIN COMPLEX

+
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