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- PDB-6coy: Human CLC-1 chloride ion channel, transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 6coy
TitleHuman CLC-1 chloride ion channel, transmembrane domain
ComponentsChloride channel protein 1
KeywordsTRANSPORT PROTEIN / chloride / channel / CLC
Function / homology
Function and homology information


voltage-gated chloride channel activity / neuronal action potential propagation / chloride transport / chloride channel complex / chloride transmembrane transport / muscle contraction / sarcolemma / Stimuli-sensing channels / protein homodimerization activity / plasma membrane
Similarity search - Function
Chloride channel ClC-1 / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / CBS domain profile.
Similarity search - Domain/homology
Chloride channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsPark, E. / MacKinnon, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2018
Title: Structure of the CLC-1 chloride channel from .
Authors: Eunyong Park / Roderick MacKinnon /
Abstract: CLC channels mediate passive Cl conduction, while CLC transporters mediate active Cl transport coupled to H transport in the opposite direction. The distinction between CLC-0/1/2 channels and CLC ...CLC channels mediate passive Cl conduction, while CLC transporters mediate active Cl transport coupled to H transport in the opposite direction. The distinction between CLC-0/1/2 channels and CLC transporters seems undetectable by amino acid sequence. To understand why they are different functionally we determined the structure of the human CLC-1 channel. Its 'glutamate gate' residue, known to mediate proton transfer in CLC transporters, adopts a location in the structure that appears to preclude it from its transport function. Furthermore, smaller side chains produce a wider pore near the intracellular surface, potentially reducing a kinetic barrier for Cl conduction. When the corresponding residues are mutated in a transporter, it is converted to a channel. Finally, Cl at key sites in the pore appear to interact with reduced affinity compared to transporters. Thus, subtle differences in glutamate gate conformation, internal pore diameter and Cl affinity distinguish CLC channels and transporters.
History
DepositionMar 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Chloride channel protein 1
B: Chloride channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,6086
Polymers217,4662
Non-polymers1424
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Chloride channel protein 1 / / ClC-1 / Chloride channel protein / skeletal muscle


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: Homo sapiens (human) / References: UniProt: P35523
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human CLC-1 chloride ion channel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13Rosettamodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175613 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL

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