[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

TitleCalcium stabilizes the flexible N-terminal domain of the bacterial ion channel DeCLIC.
Journal, issue, pagesJ Struct Biol X, Vol. 12, Page 100139, Year 2025
Publish dateNov 12, 2025
AuthorsChen Fan / Marie Lycksell / Yuxuan Zhuang / Rebecca J Howard / Erik Lindahl /
PubMed AbstractPentameric ligand-gated ion channels (pLGICs) are responsible for the rapid conversion of chemical to electrical signals. In addition to the canonical extracellular and transmembrane domains, some ...Pentameric ligand-gated ion channels (pLGICs) are responsible for the rapid conversion of chemical to electrical signals. In addition to the canonical extracellular and transmembrane domains, some prokaryotic pLGICs contain an N-terminal domain (NTD) of unclear structure and function. In one such case, the calcium-sensitive channel DeCLIC, the NTD appears to accelerate gating; however, its evident flexibility has posed a challenge to model building, and its role in calcium sensitivity is unclear. Here we report cryo-EM structures of DeCLIC in circularized lipid nanodiscs, achieving the highest resolution reported so far, and enabling definition of calcium-binding sites in both the N-terminal and canonical extracellular domains. In addition to the symmetric state, calcium depletion promoted an asymmetric conformation of the NTD, offering a structural rationale for small-angle scattering results. Behavior of these structures in molecular dynamics simulations demonstrated calcium stabilization of the NTD. These features of DeCLIC offer a model system for ion-channel modulation by a flexible accessory domain, potentially conserved in structurally homologous systems across evolution.
External linksJ Struct Biol X / PubMed:41328424 / PubMed Central
MethodsEM (single particle)
Resolution2.06 - 2.74 Å
Structure data

19991

9ev1

EMDB-19991, PDB-9ev1:
3DFlex refinement of the CryoEM structure of DeCLIC nanodisc with 10mM EDTA in sym-like state
Method: EM (single particle) / Resolution: 2.63 Å

19993

9ev7

EMDB-19993, PDB-9ev7:
3DFlex refinement of the CryoEM structure of DeCLIC nanodisc with 10mM EDTA in asym state
Method: EM (single particle) / Resolution: 2.74 Å

19994

9ev8

EMDB-19994, PDB-9ev8:
Non-uniform refinement of the CryoEM structure of DeCLIC nanodisc with 10mM calcium
Method: EM (single particle) / Resolution: 2.06 Å

19995

9ev9

EMDB-19995, PDB-9ev9:
Non-uniform refinement of the CryoEM structure of DeCLIC nanodisc with 10mM EDTA in asym state
Method: EM (single particle) / Resolution: 2.68 Å

19996

9eva

EMDB-19996, PDB-9eva:
3DFlex refinement of the CryoEM structure of DeCLIC nanodisc with 10mM calcium
Method: EM (single particle) / Resolution: 2.34 Å

19997

9evb

EMDB-19997, PDB-9evb:
Non-uniform refinement of the CryoEM structure of DeCLIC nanodisc with 10mM EDTA in sym-like state
Method: EM (single particle) / Resolution: 2.38 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-OCT:
N-OCTANE

ChemComp-D12:
DODECANE

ChemComp-D10:
DECANE

ChemComp-C14:
TETRADECANE

ChemComp-PX6:
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE

ChemComp-HOH:
WATER

Source
  • desulfofustis sp. pb-srb1 (bacteria)
KeywordsTRANSLOCASE / Ion channel

+
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