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

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Basic information

Entry
Database: PDB / ID: 9ipm
TitleHemichannel sub-structure of Cx36/GJD2 gap junction intercellular channel (FN conformation) in soybean polar lipid nanodiscs, treated with a 20-fold molar excess of carbenoxolone
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: 3.56 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
E: Gap junction delta-2 protein,Soluble cytochrome b562
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,53824
Polymers246,2136
Non-polymers9,32618
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.: 12 / 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 20-fold molar excess to Cx36 protomer.
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293E
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.: 2.54 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: 120000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 6.76 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 6001
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5096 / Height: 4092

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1648256
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111066 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049216
ELECTRON MICROSCOPYf_angle_d1.26112534
ELECTRON MICROSCOPYf_dihedral_angle_d23.6321626
ELECTRON MICROSCOPYf_chiral_restr0.1651422
ELECTRON MICROSCOPYf_plane_restr0.0041470

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