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- PDB-9ipn: Hemichannel sub-structure of Cx36/GJD2 gap junction intercellular... -

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Basic information

Entry
Database: PDB / ID: 9ipn
TitleHemichannel sub-structure of Cx36/GJD2 gap junction intercellular channel (FN conformation) in soybean polar lipid nanodiscs, treated with a 10-fold molar excess of carbenoxolone and incubated shortly
ComponentsGap junction delta-2 protein,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / Gap junction / Connexin36 / Inhibitor / Carbenoxolone
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 / electron transport chain / cell-cell signaling / chemical synaptic transmission / electron transfer activity ...Electric Transmission Across Gap Junctions / connexin complex / Gap junction assembly / gap junction channel activity / neuronal action potential / visual perception / electron transport chain / cell-cell signaling / chemical synaptic transmission / electron transfer activity / periplasmic space / iron ion binding / heme binding / synapse / plasma membrane
Similarity search - Function
Gap junction delta-2 protein (Cx36) / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues ...Gap junction delta-2 protein (Cx36) / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
TETRADECANE / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Soluble cytochrome b562 / Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsJang, H.S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00217798 Korea, Republic Of
Other privateSUHF-18010097 Korea, Republic Of
Other private Korea, Republic Of
CitationJournal: To Be Published
Title: Structural insights into the closing mechanism of gap junction intercellular channels by carbenoxolone
Authors: Lee, C.W. / Jang, H.S. / Woo, J.S.
History
DepositionJul 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gap junction delta-2 protein,Soluble cytochrome b562
B: Gap junction delta-2 protein,Soluble cytochrome b562
F: Gap junction delta-2 protein,Soluble cytochrome b562
C: Gap junction delta-2 protein,Soluble cytochrome b562
D: Gap junction delta-2 protein,Soluble cytochrome b562
E: Gap junction delta-2 protein,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,47018
Polymers246,2136
Non-polymers5,25812
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
Gap junction delta-2 protein,Soluble cytochrome b562 / Connexin-36 / Cx36 / Gap junction alpha-9 protein / Cytochrome b-562


Mass: 41035.426 Da / Num. of mol.: 6 / Mutation: M29W,H124I,R128L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: GJD2, GJA9, cybC / Plasmid: pX / Cell line (production host): HEK293E / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Kidney / References: UniProt: Q9UKL4, UniProt: P0ABE7
#2: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#3: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H30
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: Connexin36 / Type: COMPLEX
Details: BRIL-fused connexin36 gap junction intercellular channel is reconstituted into lipid nanodiscs with soybean polar lipids and MSP1E1. Carbenoxolone dissolved in 10% (v/v) DMSO is treated to ...Details: BRIL-fused connexin36 gap junction intercellular channel is reconstituted into lipid nanodiscs with soybean polar lipids and MSP1E1. Carbenoxolone dissolved in 10% (v/v) DMSO is treated to the sample with 14-fold molar excess to Cx36 protomer. Sample was incubated for 1 min before grid loading.
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293E / Plasmid: pX
Buffer solutionpH: 7.5
Details: 20mM HEPES(pH 7.5), 150mM KCl, 2mM beta-mercaptoethanol
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMPotassium chlorideKCl1
32 mMbeta-mercaptoethanolC2H6OS1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2250 nm / Nominal defocus min: 750 nm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 6.79 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5001
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
8PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2151580
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75602 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069024
ELECTRON MICROSCOPYf_angle_d0.92912282
ELECTRON MICROSCOPYf_dihedral_angle_d17.381608
ELECTRON MICROSCOPYf_chiral_restr0.1481398
ELECTRON MICROSCOPYf_plane_restr0.0051452

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