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TitleBiophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 119, Issue 50, Page e2210669119, Year 2022
Publish dateDec 13, 2022
AuthorsMarie Lycksell / Urška Rovšnik / Anton Hanke / Anne Martel / Rebecca J Howard / Erik Lindahl /
PubMed AbstractPentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in organisms ranging from bacteria to humans. Among the prokaryotic pLGICs, there is architectural diversity ...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 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.
External linksProc Natl Acad Sci U S A / PubMed:36480474 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 3.5 Å
Structure data

13791

7q3g

EMDB-13791, PDB-7q3g:
Pentameric ligand-gated ion channel, DeCLIC at pH 7 with 10 mM Ca2+
Method: EM (single particle) / Resolution: 3.5 Å

13792

7q3h

EMDB-13792, PDB-7q3h:
Pentameric ligand-gated ion channel, DeCLIC at pH 7 with 10 mM EDTA
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-CA:
Unknown entry

Source
  • desulfofustis sp. pb-srb1 (bacteria)
KeywordsMEMBRANE PROTEIN / ion channel / ligand-gated channel / pentameric channel

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