9O97 | pdb_00009o97

Cryo-EM structure of CLC-ec1 at pH 3.0

• PDB DOI: https://doi.org/10.2210/pdb9O97/pdb
• EM Map EMD-70244: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-17 Released: 2026-01-07 
• Deposition Author(s): Chien, C.-T., Chiu, W., Maduke, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular mechanism of exchange coupling in CLC chloride/proton antiporters.

Aydin, D., Chien, C.T., Kreiter, J., Nava, A.R., Portasikova, J.M., Fojtik, L., Sobecks, B.L., Mosquera, C., Man, P., Dror, R.O., Chiu, W., Maduke, M.

(2026) Nat Commun 

• PubMed: 41507156 
• DOI: https://doi.org/10.1038/s41467-025-68098-1
• Primary Citation of Related Structures:  
  9O95, 9O96, 9O97, 9O98


• PubMed Abstract: 
  

  The ubiquitous CLC membrane transporters are unique in their ability to exchange anions for cations. Despite extensive study, there is no mechanistic model that fully explains their 2:1 Cl ^‒ /H ⁺ stoichiometric exchange mechanism. Here, we provide such a model. Using differential hydrogen-deuterium exchange mass spectrometry, cryo-EM structure determination, and molecular dynamics simulations, we uncovered conformational dynamics in CLC-ec1, a bacterial CLC homolog that has served as a paradigm for this family of transporters. Simulations based on a cryo-EM structure at pH 3 revealed 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. Surprisingly, these water wires occurred independently of Cl ^‒ binding, prompting us to reassess the relationship between Cl ^‒ binding and Cl ^‒ /H ⁺ coupling. Using isothermal titration calorimetry and quantitative flux assays on mutants with reduced Cl ^‒ binding affinity, we conclude that, while Cl ^‒ binding is necessary for coupling, even weak binding can support Cl ^‒ /H ⁺ coupling. By integrating our findings with existing literature, we establish a complete and efficient CLC 2:1 Cl ^‒ /H ⁺ exchange mechanism.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
Department of Computer Science, Stanford University, Stanford, CA, USA.
Department of Structural Biology, Stanford University, Stanford, CA, USA.
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
Department of Bioengineering, Stanford University, Stanford, CA, USA.
Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA.
Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic.
Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, Vestec, Czech Republic.
Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA. [e-mail].
Department of Computer Science, Stanford University, Stanford, CA, USA. [e-mail].
Department of Structural Biology, Stanford University, Stanford, CA, USA. [e-mail].
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA. [e-mail].
Department of Bioengineering, Stanford University, Stanford, CA, USA. [e-mail].
Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA. [e-mail].
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 104.44 kDa 
• Atom Count: 6,488 
• Modeled Residue Count: 870 
• Deposited Residue Count: 978 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(+)/Cl(-) exchange transporter ClcA	A, B	489	Escherichia coli	Mutation(s): 0  Gene Names: clcA, eriC, yadQ, b0155, JW5012
UniProt
Find proteins for P37019 (Escherichia coli (strain K12)) Explore P37019  Go to UniProtKB:  P37019

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-07 
Deposition Author(s): Chien, C.-T., Chiu, W., Maduke, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM113195

Revision History  

• Version 1.0: 2026-01-07
  Type: Initial release
  
• Version 1.1: 2026-01-21
  Changes: Data collection, Database references