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- PDB-7xja: TMD masked refine map of human ClC-2 -

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Basic information

Entry
Database: PDB / ID: 7xja
TitleTMD masked refine map of human ClC-2
ComponentsChloride channel protein 2
KeywordsMEMBRANE PROTEIN / homo-dimer
Function / homology
Function and homology information


regulation of aldosterone biosynthetic process / cell differentiation involved in salivary gland development / regulation of membrane depolarization during action potential / volume-sensitive chloride channel activity / stabilization of membrane potential / astrocyte end-foot / acinar cell differentiation / cellular hypotonic response / regulation of resting membrane potential / voltage-gated chloride channel activity ...regulation of aldosterone biosynthetic process / cell differentiation involved in salivary gland development / regulation of membrane depolarization during action potential / volume-sensitive chloride channel activity / stabilization of membrane potential / astrocyte end-foot / acinar cell differentiation / cellular hypotonic response / regulation of resting membrane potential / voltage-gated chloride channel activity / axon initial segment / dendritic spine membrane / chloride channel regulator activity / chloride transport / phagocytosis, engulfment / positive regulation of oligodendrocyte differentiation / chloride channel complex / lung development / Stimuli-sensing channels / myelin sheath / retina development in camera-type eye / basolateral plasma membrane / perikaryon / postsynaptic membrane / plasma membrane
Similarity search - Function
Chloride channel ClC-2 / : / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily / CBS domain profile.
Similarity search - Domain/homology
Chloride channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structures of ClC-2 chloride channel reveal the blocking mechanism of its specific inhibitor AK-42
Authors: Ma, T. / Wang, L. / Chai, A. / Liu, C. / Cui, W. / Yuan, S. / Wing Ngor Au, S. / Sun, L. / Zhang, X. / Zhang, Z. / Lu, J. / Gao, Y. / Wang, P. / Li, Z. / Liang, Y. / Vogel, H. / Wang, Y.T. / ...Authors: Ma, T. / Wang, L. / Chai, A. / Liu, C. / Cui, W. / Yuan, S. / Wing Ngor Au, S. / Sun, L. / Zhang, X. / Zhang, Z. / Lu, J. / Gao, Y. / Wang, P. / Li, Z. / Liang, Y. / Vogel, H. / Wang, Y.T. / Wang, D. / Yan, K. / Zhang, H.
History
DepositionApr 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 17, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / 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: Chloride channel protein 2
B: Chloride channel protein 2


Theoretical massNumber of molelcules
Total (without water)197,2852
Polymers197,2852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4400 Å2
ΔGint-49 kcal/mol
Surface area39520 Å2

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Components

#1: Protein Chloride channel protein 2 / ClC-2


Mass: 98642.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLCN2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P51788
Has protein modificationN

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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: Full length human CLC-2 homo dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 180 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43510 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027462
ELECTRON MICROSCOPYf_angle_d0.54310164
ELECTRON MICROSCOPYf_dihedral_angle_d3.9411004
ELECTRON MICROSCOPYf_chiral_restr0.0391200
ELECTRON MICROSCOPYf_plane_restr0.0041258

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