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- PDB-8jpr: Cryo-EM structure of Y553C human ClC-6 -

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Basic information

Entry
Database: PDB / ID: 8jpr
TitleCryo-EM structure of Y553C human ClC-6
ComponentsH(+)/Cl(-) exchange transporter 6
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


voltage-gated chloride channel activity / cell volume homeostasis / chloride transport / chloride transmembrane transporter activity / antiporter activity / response to mechanical stimulus / Stimuli-sensing channels / late endosome membrane / Signaling by BRAF and RAF1 fusions / monoatomic ion transmembrane transport ...voltage-gated chloride channel activity / cell volume homeostasis / chloride transport / chloride transmembrane transporter activity / antiporter activity / response to mechanical stimulus / Stimuli-sensing channels / late endosome membrane / Signaling by BRAF and RAF1 fusions / monoatomic ion transmembrane transport / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / signal transduction / ATP binding / membrane
Similarity search - Function
Chloride channel ClC-6 / : / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / H(+)/Cl(-) exchange transporter 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang, S.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030056 China
CitationJournal: Sci Adv / Year: 2023
Title: Molecular basis of ClC-6 function and its impairment in human disease
Authors: Zhang, S.S.
History
DepositionJun 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.0Sep 20, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 20, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Sep 20, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 20, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 20, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 20, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 20, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 20, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 25, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H(+)/Cl(-) exchange transporter 6
B: H(+)/Cl(-) exchange transporter 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,85210
Polymers194,6472
Non-polymers1,2058
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein H(+)/Cl(-) exchange transporter 6 / Chloride channel protein 6 / ClC-6 / Chloride transport protein 6


Mass: 97323.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLCN6, KIAA0046 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P51797
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN
Has protein modificationY

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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: endolysosomal transporter / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311646
ELECTRON MICROSCOPYf_angle_d0.51315804
ELECTRON MICROSCOPYf_dihedral_angle_d4.2331570
ELECTRON MICROSCOPYf_chiral_restr0.0391832
ELECTRON MICROSCOPYf_plane_restr0.0041976

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