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- PDB-8jgv: Cryo-EM structure of mClC-3_I607T with ATP -

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Basic information

Entry
Database: PDB / ID: 8jgv
TitleCryo-EM structure of mClC-3_I607T with ATP
ComponentsH(+)/Cl(-) exchange transporter 3
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


volume-sensitive chloride channel activity / chloride:proton antiporter activity / synaptic vesicle lumen acidification / inhibitory synapse / negative regulation of cell volume / voltage-gated chloride channel activity / specific granule / photoreceptor cell maintenance / vesicle membrane / antiporter activity ...volume-sensitive chloride channel activity / chloride:proton antiporter activity / synaptic vesicle lumen acidification / inhibitory synapse / negative regulation of cell volume / voltage-gated chloride channel activity / specific granule / photoreceptor cell maintenance / vesicle membrane / antiporter activity / phagocytosis, engulfment / synaptic transmission, GABAergic / positive regulation of reactive oxygen species biosynthetic process / phagocytic vesicle / axon terminus / adult locomotory behavior / synaptic transmission, glutamatergic / PDZ domain binding / recycling endosome / neuron cellular homeostasis / GABA-ergic synapse / recycling endosome membrane / synaptic vesicle / synaptic vesicle membrane / late endosome membrane / late endosome / early endosome membrane / early endosome / endosome / endosome membrane / lysosomal membrane / external side of plasma membrane / glutamatergic synapse / Golgi apparatus / ATP binding / plasma membrane
Similarity search - Function
Chloride channel ClC-3 / 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 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWan, Y.Z.Q. / Yang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122040 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis of adenine nucleotides regulation and neurodegenerative pathology in ClC-3 exchanger.
Authors: Yangzhuoqun Wan / Shuangshuang Guo / Wenxuan Zhen / Lizhen Xu / Xiaoying Chen / Fangyue Liu / Yi Shen / Shuangshuang Liu / Lidan Hu / Xinyan Wang / Fengcan Ye / Qinrui Wang / Han Wen / Fan Yang /
Abstract: The ClC-3 chloride/proton exchanger is both physiologically and pathologically critical, as it is potentiated by ATP to detect metabolic energy level and point mutations in ClC-3 lead to severe ...The ClC-3 chloride/proton exchanger is both physiologically and pathologically critical, as it is potentiated by ATP to detect metabolic energy level and point mutations in ClC-3 lead to severe neurodegenerative diseases in human. However, why this exchanger is differentially modulated by ATP, ADP or AMP and how mutations caused gain-of-function remains largely unknow. Here we determine the high-resolution structures of dimeric wildtype ClC-3 in the apo state and in complex with ATP, ADP and AMP, and the disease-causing I607T mutant in the apo and ATP-bounded state by cryo-electron microscopy. In combination with patch-clamp recordings and molecular dynamic simulations, we reveal how the adenine nucleotides binds to ClC-3 and changes in ion occupancy between apo and ATP-bounded state. We further observe I607T mutation induced conformational changes and augments in current. Therefore, our study not only lays the structural basis of adenine nucleotides regulation in ClC-3, but also clearly indicates the target region for drug discovery against ClC-3 mediated neurodegenerative diseases.
History
DepositionMay 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Sep 4, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 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 3
B: H(+)/Cl(-) exchange transporter 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,9064
Polymers181,8922
Non-polymers1,0142
Water00
1


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

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Components

#1: Protein H(+)/Cl(-) exchange transporter 3 / Chloride channel protein 3 / ClC-3 / Chloride transporter ClC-3


Mass: 90945.766 Da / Num. of mol.: 2 / Fragment: I607T, I790R, V791L / Mutation: I607T, I790R, V791L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clcn3, Clc3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P51791
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
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: mClC-3_I607T with ATP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 5 mg/ml / Embedding 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: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57969 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410864
ELECTRON MICROSCOPYf_angle_d0.61414760
ELECTRON MICROSCOPYf_dihedral_angle_d4.521450
ELECTRON MICROSCOPYf_chiral_restr0.0411666
ELECTRON MICROSCOPYf_plane_restr0.0041802

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