+Open data
-Basic information
Entry | Database: PDB / ID: 8gqu | ||||||
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Title | AK-42 inhibitor binding human ClC-2 TMD | ||||||
Components | Chloride channel protein 2 | ||||||
Keywords | MEMBRANE PROTEIN / homo-dimer | ||||||
Function / homology | Function and homology information regulation of aldosterone biosynthetic process / cell differentiation involved in salivary gland development / acinar cell differentiation / voltage-gated chloride channel activity / chloride transport / positive regulation of oligodendrocyte differentiation / chloride channel complex / lung development / Stimuli-sensing channels / retina development in camera-type eye ...regulation of aldosterone biosynthetic process / cell differentiation involved in salivary gland development / acinar cell differentiation / voltage-gated chloride channel activity / chloride transport / positive regulation of oligodendrocyte differentiation / chloride channel complex / lung development / Stimuli-sensing channels / retina development in camera-type eye / perikaryon / dendrite / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Wang, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structures of ClC-2 chloride channel reveal the blocking mechanism of its specific inhibitor AK-42. Authors: Tao Ma / Lei Wang / Anping Chai / Chao Liu / Wenqiang Cui / Shuguang Yuan / Shannon Wing Ngor Au / Liang Sun / Xiaokang Zhang / Zhenzhen Zhang / Jianping Lu / Yuanzhu Gao / Peiyi Wang / ...Authors: Tao Ma / Lei Wang / Anping Chai / Chao Liu / Wenqiang Cui / Shuguang Yuan / Shannon Wing Ngor Au / Liang Sun / Xiaokang Zhang / Zhenzhen Zhang / Jianping Lu / Yuanzhu Gao / Peiyi Wang / Zhifang Li / Yujie Liang / Horst Vogel / Yu Tian Wang / Daping Wang / Kaige Yan / Huawei Zhang / Abstract: ClC-2 transports chloride ions across plasma membranes and plays critical roles in cellular homeostasis. Its dysfunction is involved in diseases including leukodystrophy and primary aldosteronism. AK- ...ClC-2 transports chloride ions across plasma membranes and plays critical roles in cellular homeostasis. Its dysfunction is involved in diseases including leukodystrophy and primary aldosteronism. AK-42 was recently reported as a specific inhibitor of ClC-2. However, experimental structures are still missing to decipher its inhibition mechanism. Here, we present cryo-EM structures of apo ClC-2 and its complex with AK-42, both at 3.5 Å resolution. Residues S162, E205 and Y553 are involved in chloride binding and contribute to the ion selectivity. The side-chain of the gating glutamate E205 occupies the putative central chloride-binding site, indicating that our structure represents a closed state. Structural analysis, molecular dynamics and electrophysiological recordings identify key residues to interact with AK-42. Several AK-42 interacting residues are present in ClC-2 but not in other ClCs, providing a possible explanation for AK-42 specificity. Taken together, our results experimentally reveal the potential inhibition mechanism of ClC-2 inhibitor AK-42. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gqu.cif.gz | 183.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gqu.ent.gz | 138.2 KB | Display | PDB format |
PDBx/mmJSON format | 8gqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/8gqu ftp://data.pdbj.org/pub/pdb/validation_reports/gq/8gqu | HTTPS FTP |
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-Related structure data
Related structure data | 34202MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 98642.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLCN2 / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: P51788 #2: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: AK-42 inhibitor binding human ClC-2 TMD 3.5A / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 180 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293F |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44153 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |