PXD058693-1

PXD058693 is an original dataset announced via ProteomeXchange.

Title	Molecular mechanism of exchange coupling in CLC chloride/proton antiporters
Description	The ubiquitous CLC membrane transporters are the only transporter family known to exchange anions for cations. Despite extensive study, there is no model to completely explain the 2:1 Cl‒/H+ stoichiometric exchange mechanism. Here, we provide such a model. Using CLC-ec1, a bacterial homolog that has served as a paradigm for the family, we determined cryo-EM structures at pH 7, pH 4.5, and pH 3. Molecular dynamics simulations of the pH-3 structure reveal critical steps in the transport mechanism, including release of Cl- ions to the extracellular side, opening of the inner gate, and water wires that facilitate H+ transport. Water wires are observed frequently in both the canonical H+-transport pathway and in the Cl- pathway, where they had not been previously reported. We propose that tight coupling of Cl‒/H+ transport is maintained (uncoupled H+ transport is avoided) because H+ transfer from the water wires to the catalytic glutamate is favored only when Cl‒ is also present in the pathway . Mutations that weaken Cl‒ binding without changing the pathway structure exhibit functional properties consistent with this model.
HostingRepository	PRIDE
AnnounceDate	2025-07-21
AnnouncementXML	Submission_2025-07-20_16:12:58.841.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jasmína Portašiková
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-09 04:50:18	ID requested
⏵ 1	2025-07-20 16:12:59	announced

Hu Q, Huang T, Zhu A, Angl, é, s A, Abdelghany O, Ahmed A, Fern, á, ndez-Remolar DC, Comparing Protein Stability in Modern and Ancient Sabkha Environments: Implications for Molecular Remnants on Ancient Mars. Int J Mol Sci, 26(13):(2025) [pubmed]

10.3390/ijms26135978;

submitter keyword: mass spectrometry, protein structure, membrane proteins,H/D exchange, proton-chloride antiporter

Petr Man
contact affiliation	Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic
contact email	pman@biomed.cas.cz
lab head
Jasmína Portašiková
contact affiliation	Charles University, Faculty of Science, Prague, Czech Republic
contact email	portasij@natur.cuni.cz
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/07/PXD058693

PRIDE project URI

• PRIDE
  1. PXD058693
     1. Label: PRIDE project
     2. Name: Molecular mechanism of exchange coupling in CLC chloride/proton antiporters