Pentameric ligand-gated ion channel, DeCLIC at pH 7 with 10 mM EDTA

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel.

Lycksell, M.Rovsnik, U.Hanke, A.Martel, A.Howard, R.J.Lindahl, E.

(2022) Proc Natl Acad Sci U S A 119: e2210669119-e2210669119

  • DOI: https://doi.org/10.1073/pnas.2210669119
  • Primary Citation of Related Structures:  
    7Q3G, 7Q3H

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in organisms ranging from bacteria to humans. Among the prokaryotic pLGICs, there is architectural diversity involving N-terminal domains (NTDs) not found in eukaryotic relatives, exemplified by the calcium-sensitive channel (DeCLIC) from a Desulfofustis deltaproteobacterium, which has an NTD in addition to the canonical pLGIC structure. Here, we have characterized the structure and dynamics of DeCLIC through cryoelectron microscopy (cryo-EM), small-angle neutron scattering (SANS), and molecular dynamics (MD) simulations. In the presence and absence of calcium, cryo-EM yielded structures with alternative conformations of the calcium-binding site. SANS profiles further revealed conformational diversity at room temperature beyond that observed in static structures, shown through MD to be largely attributable to rigid-body motions of the NTD relative to the protein core, with expanded and asymmetric conformations improving the fit of the SANS data. This work reveals the range of motion available to the DeCLIC NTD and calcium-binding site, expanding the conformational landscape of the pLGIC family. Further, these findings demonstrate the power of combining low-resolution scattering, high-resolution structural, and MD simulation data to elucidate interfacial interactions that are highly conserved in the pLGIC family.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neur_chan_LBD domain-containing proteinA,
B [auth E],
C [auth D],
D [auth C],
E [auth B]
642Desulfofustis sp. PB-SRB1Mutation(s): 0 
Gene Names: N839_03575
Membrane Entity: Yes 
Find proteins for V4JF97 (Desulfofustis sp. PB-SRB1)
Explore V4JF97 
Go to UniProtKB:  V4JF97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV4JF97
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
Swedish Research CouncilSweden--
The Swedish Foundation for Strategic ResearchSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references