9EVA
3DFlex refinement of the CryoEM structure of DeCLIC nanodisc with 10mM calcium
This is a non-PDB format compatible entry.
Summary for 9EVA
| Entry DOI | 10.2210/pdb9eva/pdb |
| EMDB information | 19996 |
| Descriptor | Neur_chan_LBD domain-containing protein, CALCIUM ION (2 entities in total) |
| Functional Keywords | ion channel, translocase |
| Biological source | Desulfofustis sp. PB-SRB1 |
| Total number of polymer chains | 5 |
| Total formula weight | 359070.74 |
| Authors | Fan, C.,Howard, R.J.,Lindahl, E. (deposition date: 2024-03-28, release date: 2025-04-09, Last modification date: 2025-12-17) |
| Primary citation | Fan, C.,Lycksell, M.,Zhuang, Y.,Howard, R.J.,Lindahl, E. Calcium stabilizes the flexible N-terminal domain of the bacterial ion channel DeCLIC. J Struct Biol X, 12:100139-100139, 2025 Cited by PubMed Abstract: 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. PubMed: 41328424DOI: 10.1016/j.yjsbx.2025.100139 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.34 Å) |
Structure validation
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