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Yorodumi- PDB-8xgf: Human Cx36/GJD2 gap junction channel in complex with arachidonic acid. -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xgf | ||||||
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Title | Human Cx36/GJD2 gap junction channel in complex with arachidonic acid. | ||||||
Components | Gap junction delta-2 protein | ||||||
Keywords | MEMBRANE PROTEIN / connexin 36 / Gap Junction Channel / Cx36 / GJD2 / arachidonic acid | ||||||
Function / homology | Function and homology information Electric Transmission Across Gap Junctions / connexin complex / Gap junction assembly / gap junction channel activity / neuronal action potential / visual perception / cell-cell signaling / chemical synaptic transmission / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å | ||||||
Authors | Cho, H.J. / Lee, H.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Mefloquine-induced conformational shift in Cx36 N-terminal helix leading to channel closure mediated by lipid bilayer. Authors: Hwa-Jin Cho / Dong Kyu Chung / Hyung Ho Lee / Abstract: Connexin 36 (Cx36) forms interneuronal gap junctions, establishing electrical synapses for rapid synaptic transmission. In disease conditions, inhibiting Cx36 gap junction channels (GJCs) is ...Connexin 36 (Cx36) forms interneuronal gap junctions, establishing electrical synapses for rapid synaptic transmission. In disease conditions, inhibiting Cx36 gap junction channels (GJCs) is beneficial, as it prevents abnormal synchronous neuronal firing and apoptotic signal propagation, mitigating seizures and progressive cell death. Here, we present cryo-electron microscopy structures of human Cx36 GJC in complex with known channel inhibitors, such as mefloquine, arachidonic acid, and 1-hexanol. Notably, these inhibitors competitively bind to the binding pocket of the N-terminal helices (NTH), inducing a conformational shift from the pore-lining NTH (PLN) state to the flexible NTH (FN) state. This leads to the obstruction of the channel pore by flat double-layer densities of lipids. These studies elucidate the molecular mechanisms of how Cx36 GJC can be modulated by inhibitors, providing valuable insights into potential therapeutic applications. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xgf.cif.gz | 814.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xgf.ent.gz | 668.3 KB | Display | PDB format |
PDBx/mmJSON format | 8xgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xgf_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 8xgf_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8xgf_validation.xml.gz | 74.9 KB | Display | |
Data in CIF | 8xgf_validation.cif.gz | 92.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/8xgf ftp://data.pdbj.org/pub/pdb/validation_reports/xg/8xgf | HTTPS FTP |
-Related structure data
Related structure data | 38320MC 8xgdC 8xgeC 8xggC 8xgjC 8xh8C 8xh9C 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: 37376.910 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: Residues M1-V321: connexin 36 Residues S322-R323: linker Residues D324-K331: affinity tag (FLAG) Following regions are not modeled because of ambiguity of density map: Residues M1-H19, S101-I195, and G276-K331) Source: (gene. exp.) Homo sapiens (human) / Gene: GJD2, GJA9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UKL4 #2: Chemical | ChemComp-MC3 / #3: Chemical | ChemComp-ACD / Has ligand of interest | Y | Has protein modification | 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: Human Cx36/GJD2 gap junction channel / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68143 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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