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- EMDB-4647: CryoEM structure of the human ClC-1 chloride channel, CBS state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-4647
TitleCryoEM structure of the human ClC-1 chloride channel, CBS state 1
Map data
Samplehuman Chloride Channel protein 1:
Chloride channel protein 1
Function / homology
Function and homology information


Stimuli-sensing channels / voltage-gated chloride channel activity / neuronal action potential propagation / chloride channel complex / chloride transmembrane transport / regulation of ion transmembrane transport / ion transmembrane transport / muscle contraction / sarcolemma / integral component of plasma membrane ...Stimuli-sensing channels / voltage-gated chloride channel activity / neuronal action potential propagation / chloride channel complex / chloride transmembrane transport / regulation of ion transmembrane transport / ion transmembrane transport / muscle contraction / sarcolemma / integral component of plasma membrane / protein homodimerization activity / plasma membrane
CBS domain profile. / CBS domain / Chloride channel, voltage gated / Chloride channel ClC-1 / Chloride channel, core / Voltage gated chloride channel
Chloride channel protein 1
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsWang KT / Gourdon PE / Zhou ZH
CitationJournal: 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 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.
Validation ReportPDB-ID: 6qvc

SummaryFull reportAbout validation report
DateDeposition: Mar 1, 2019 / Header (metadata) release: May 8, 2019 / Map release: May 8, 2019 / Update: May 8, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6qvc
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_4647.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 288 pix.
= 308.16 Å
1.07 Å/pix.
x 288 pix.
= 308.16 Å
1.07 Å/pix.
x 288 pix.
= 308.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.03
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.023208953 (±0.14658363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 308.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z308.160308.160308.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0520.1060.000

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Supplemental data

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Mask #1

Fileemd_4647_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire human Chloride Channel protein 1

EntireName: human Chloride Channel protein 1 / Number of components: 2

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Component #1: protein, human Chloride Channel protein 1

ProteinName: human Chloride Channel protein 1 / Recombinant expression: No
MassTheoretical: 109 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, Chloride channel protein 1

ProteinName: Chloride channel protein 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 108.733172 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.6 mg/mL / Buffer solution: 20mM Tris ph7.5 100mM NaCl 0.2mM TCEP / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: OTHER
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 176871
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5TQQ
Output model

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