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Yorodumi- PDB-6qv6: CryoEM structure of the human ClC-1 chloride channel, membrane domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qv6 | ||||||
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Title | CryoEM structure of the human ClC-1 chloride channel, membrane domain | ||||||
Components | Chloride channel protein 1 | ||||||
Keywords | MEMBRANE PROTEIN / chloride channel / CLC1 / CLCN1 | ||||||
Function / homology | Function and homology information voltage-gated chloride channel activity / neuronal action potential propagation / chloride transport / chloride channel complex / muscle contraction / chloride transmembrane transport / T-tubule / Stimuli-sensing channels / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å | ||||||
Authors | Wang, K.T. / Gourdon, P.E. / Zhou, Z.H. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: PLoS Biol / Year: 2019 Title: Structure of the human ClC-1 chloride channel. Authors: Kaituo Wang / Sarah Spruce Preisler / Liying Zhang / Yanxiang Cui / Julie Winkel Missel / Christina Grønberg / Kamil Gotfryd / Erik Lindahl / Magnus Andersson / Kirstine Calloe / Pascal F ...Authors: Kaituo Wang / Sarah Spruce Preisler / Liying Zhang / Yanxiang Cui / Julie Winkel Missel / Christina Grønberg / Kamil Gotfryd / Erik Lindahl / Magnus Andersson / Kirstine Calloe / Pascal F Egea / Dan Arne Klaerke / Michael Pusch / Per Amstrup Pedersen / Z Hong Zhou / Pontus Gourdon / 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 ...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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6qv6.cif.gz | 184.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qv6.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 6qv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qv6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6qv6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6qv6_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 6qv6_validation.cif.gz | 60.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/6qv6 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/6qv6 | HTTPS FTP |
-Related structure data
Related structure data | 4645MC 4646C 4647C 4649C 4657C 6qvbC 6qvcC 6qvdC 6qvuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 108733.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLCN1, CLC1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35523 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human Chloride Channel protein 1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.109 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 / Details: 20mM Tris ph7.5 100mM NaCl 0.2mM TCEP |
Buffer component | Conc.: 20 mM / Name: Tris |
Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 9 sec. / Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 60 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 477729 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176871 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5TQQ Accession code: 5TQQ / Source name: PDB / Type: experimental model |