8TA2

Cryo-EM structure of the human CLC-2 chloride channel transmembrane domain with bound inhibitor AK-42

Summary for 8TA2

• Entry DOI: 10.2210/pdb8ta2/pdb
• EMDB information: 41126 41127 41128 41129 41130
• Descriptor: Chloride channel protein 2, 2-[[2,6-bis(chloranyl)-3-phenylmethoxy-phenyl]amino]pyridine-3-carboxylic acid, CHLORIDE ION (3 entities in total)
• Functional Keywords: chloride, channel, inhibitor, protein, voltage gated, transport protein-inhibitor complex, transport protein/inhibitor
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 105630.71

Authors

Xu, M.,Neelands, T.,Powers, A.S.,Liu, Y.,Miller, S.,Pintilie, G.,Du Bois, J.,Dror, R.O.,Chiu, W.,Maduke, M. (deposition date: 2023-06-26, release date: 2024-01-31, Last modification date: 2024-02-28)

Primary citation

Xu, M.,Neelands, T.,Powers, A.S.,Liu, Y.,Miller, S.D.,Pintilie, G.D.,Bois, J.D.,Dror, R.O.,Chiu, W.,Maduke, M.
CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism.
Elife, 12:-, 2024

PubMed Abstract: CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating among closely related homologs has been a long-standing mystery, in part because few CLC channel structures are available. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 Å, in the presence and absence of the selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl-permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct conformations involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl-permeation pathway. This peptide is highly conserved among species variants of CLC-2 but is not present in other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl-permeation pathway.

PubMed: 38345841
DOI: 10.7554/eLife.90648

Experimental method

ELECTRON MICROSCOPY (2.74 Å)