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- EMDB-70242: Cryo-EM structure of CLC-ec1 at pH 7.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-70242
TitleCryo-EM structure of CLC-ec1 at pH 7.5
Map data
Sample
  • Complex: H(+)/Cl(-) exchange transporter ClcA
    • Protein or peptide: H(+)/Cl(-) exchange transporter ClcA
  • Ligand: CHLORIDE ION
Keywordstransmembrane protein cryo-EM Antiporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


cellular stress response to acidic pH / chloride:proton antiporter activity / voltage-gated chloride channel activity / proton transmembrane transport / chloride transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel
Similarity search - Domain/homology
H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChien C-T / Chiu W / Maduke M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM113195 United States
CitationJournal: Nat Commun / Year: 2026
Title: Molecular mechanism of exchange coupling in CLC chloride/proton antiporters.
Authors: Deniz Aydin / Chih-Ta Chien / Jürgen Kreiter / Amy R Nava / Jasmina M Portasikova / Lukas Fojtik / Briana L Sobecks / Catalina Mosquera / Petr Man / Ron O Dror / Wah Chiu / Merritt Maduke /
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 ...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.
History
DepositionApr 17, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70242.png

Downloads & links

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Map

FileDownload / File: emd_70242.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.19
Minimum - Maximum-5.671277 - 8.650706
Average (Standard dev.)0.0022360357 (±0.22303084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70242_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70242_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : H(+)/Cl(-) exchange transporter ClcA

EntireName: H(+)/Cl(-) exchange transporter ClcA
Components
  • Complex: H(+)/Cl(-) exchange transporter ClcA
    • Protein or peptide: H(+)/Cl(-) exchange transporter ClcA
  • Ligand: CHLORIDE ION

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Supramolecule #1: H(+)/Cl(-) exchange transporter ClcA

SupramoleculeName: H(+)/Cl(-) exchange transporter ClcA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: H(+)/Cl(-) exchange transporter ClcA

MacromoleculeName: H(+)/Cl(-) exchange transporter ClcA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 52.115359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKTDTPSLET PQAARLRRRQ LIRQLLERDK TPLAILFMAA VVGTLVGLAA VAFDKGVAWL QNQRMGALVH TADNYPLLLT VAFLCSAVL AMFGYFLVRK YAPEAGGSGI PEIEGALEDQ RPVRWWRVLP VKFFGGLGTL GGGMVLGREG PTVQIGGNIG R MVLDIFRL ...String:
MKTDTPSLET PQAARLRRRQ LIRQLLERDK TPLAILFMAA VVGTLVGLAA VAFDKGVAWL QNQRMGALVH TADNYPLLLT VAFLCSAVL AMFGYFLVRK YAPEAGGSGI PEIEGALEDQ RPVRWWRVLP VKFFGGLGTL GGGMVLGREG PTVQIGGNIG R MVLDIFRL KGDEARHTLL ATGAAAGLAA AFNAPLAGIL FIIEEMRPQF RYTLISIKAV FIGVIMSTIM YRIFNHEVAL ID VGKLSDA PLNTLWLYLI LGIIFGIFGP IFNKWVLGMQ DLLHRVHGGN ITKWVLMGGA IGGLCGLLGF VAPATSGGGF NLI PIATAG NFSMGMLVFI FVARVITTLL CFSSGAPGGI FAPMLALGTV LGTAFGMVAV ELFPQYHLEA GTFAIAGMGA LLAA SIRAP LTGIILVLEM TDNYQLILPM IITGLGATLL AQFTGGKPLY SAILARTLAK QEAEQLARSK AASKGSGTLV PRGSG GLEH HHHHH

UniProtKB: H(+)/Cl(-) exchange transporter ClcA

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1ots

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72103
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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