8IAD

The Arabidopsis CLCa transporter bound with nitrate, ATP and PIP2

Summary for 8IAD

• Entry DOI: 10.2210/pdb8iad/pdb
• EMDB information: 35300
• Descriptor: Chloride channel protein CLC-a, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: transporter, atp, pip2, membrane protein
• Biological source: Arabidopsis thaliana (Thale cress)
• Total number of polymer chains: 2
• Total formula weight: 173781.94

Authors

Yang, Z.,Zhang, X.,Zhang, P. (deposition date: 2023-02-08, release date: 2023-08-02, Last modification date: 2024-10-30)

Primary citation

Yang, Z.,Zhang, X.,Ye, S.,Zheng, J.,Huang, X.,Yu, F.,Chen, Z.,Cai, S.,Zhang, P.
Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids.
Nat Commun, 14:4879-4879, 2023

PubMed Abstract: Chloride channels (CLCs) transport anion across membrane to regulate ion homeostasis and acidification of intracellular organelles, and are divided into anion channels and anion/proton antiporters. Arabidopsis thaliana CLCa (AtCLCa) transporter localizes to the tonoplast which imports NO and to a less extent Cl from cytoplasm. The activity of AtCLCa and many other CLCs is regulated by nucleotides and phospholipids, however, the molecular mechanism remains unclear. Here we determine the cryo-EM structures of AtCLCa bound with NO and Cl, respectively. Both structures are captured in ATP and PI(4,5)P bound conformation. Structural and electrophysiological analyses reveal a previously unidentified N-terminal β-hairpin that is stabilized by ATP binding to block the anion transport pathway, thereby inhibiting the AtCLCa activity. While AMP loses the inhibition capacity due to lack of the β/γ- phosphates required for β-hairpin stabilization. This well explains how AtCLCa senses the ATP/AMP status to regulate the physiological nitrogen-carbon balance. Our data further show that PI(4,5)P or PI(3,5)P binds to the AtCLCa dimer interface and occupies the proton-exit pathway, which may help to understand the inhibition of AtCLCa by phospholipids to facilitate guard cell vacuole acidification and stomatal closure. In a word, our work suggests the regulatory mechanism of AtCLCa by nucleotides and phospholipids under certain physiological scenarios and provides new insights for future study of CLCs.

PubMed: 37573431
DOI: 10.1038/s41467-023-40624-z

Experimental method

ELECTRON MICROSCOPY (3.16 Å)