6QVU | pdb_00006qvu

CryoEM structure of the human ClC-1 chloride channel, low pH

• PDB DOI: https://doi.org/10.2210/pdb6QVU/pdb
• EM Map EMD-4657: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-03-05 Released: 2019-05-08 
• Deposition Author(s): Wang, K.T., Gourdon, P.E., Zhou, Z.H.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structure of the human ClC-1 chloride channel.

Wang, K., Preisler, S.S., Zhang, L., Cui, Y., Missel, J.W., Gronberg, C., Gotfryd, K., Lindahl, E., Andersson, M., Calloe, K., Egea, P.F., Klaerke, D.A., Pusch, M., Pedersen, P.A., Zhou, Z.H., Gourdon, P.

(2019) PLoS Biol 17: e3000218-e3000218

• PubMed: 31022181 
• DOI: https://doi.org/10.1371/journal.pbio.3000218
• Primary Citation Related Structures: 
  6QV6, 6QVB, 6QVC, 6QVD, 6QVU


• PubMed Abstract: 
  

  ClC-1 protein channels facilitate rapid passage of chloride ions across cellular membranes, thereby orchestrating skeletal muscle excitability. Malfunction of ClC-1 is associated with myotonia congenita, a disease impairing muscle relaxation. Here, we present the cryo-electron microscopy (cryo-EM) structure of human ClC-1, uncovering an architecture reminiscent of that of bovine ClC-K and CLC transporters. The chloride conducting pathway exhibits distinct features, including a central glutamate residue ("fast gate") known to confer voltage-dependence (a mechanistic feature not present in ClC-K), linked to a somewhat rearranged central tyrosine and a narrower aperture of the pore toward the extracellular vestibule. These characteristics agree with the lower chloride flux of ClC-1 compared with ClC-K and enable us to propose a model for chloride passage in voltage-dependent CLC channels. Comparison of structures derived from protein studied in different experimental conditions supports the notion that pH and adenine nucleotides regulate ClC-1 through interactions between the so-called cystathionine-β-synthase (CBS) domains and the intracellular vestibule ("slow gating"). The structure also provides a framework for analysis of mutations causing myotonia congenita and reveals a striking correlation between mutated residues and the phenotypic effect on voltage gating, opening avenues for rational design of therapies against ClC-1-related diseases.

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Organizational Affiliation: 
• Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
Department of Microbiology, Immunology & Molecular Genetics, University of California at Los Angeles, Los Angeles, California.
California NanoSystems Institute, University of California at Los Angeles, Los Angeles, California.
Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.
Department of Chemistry, Umeå University, Umeå, Sweden.
Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, California.
Institute of Biophysics, Consiglio Nazionale delle Ricerche, Genova, Italy.
Department of Experimental Medical Science, Lund University, Lund, Sweden.

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 PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 217.47 kDa 
• Atom Count: 9,272 
• Modeled Residue Count: 1,198 
• Deposited Residue Count: 1,976 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloride channel protein 1	A [auth B], B [auth A]	988	Homo sapiens	Mutation(s): 0  Gene Names: CLCN1, CLC1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P35523 (Homo sapiens) Explore P35523  Go to UniProtKB:  P35523
PHAROS:  P35523 GTEx:  ENSG00000188037

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	2.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-08 
Deposition Author(s): Wang, K.T., Gourdon, P.E., Zhou, Z.H.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	4092-00228

Revision History  

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Refinement description