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- EMDB-60777: Hemichannel sub-structure of Cx36/GJD2 gap junction intercellular... -

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Basic information

Entry
Database: EMDB / ID: EMD-60777
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
Map data
Sample
  • Complex: Connexin36
    • Protein or peptide: Gap junction delta-2 protein,Soluble cytochrome b562
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: TETRADECANE
KeywordsGap junction / Connexin36 / Inhibitor / Carbenoxolone / MEMBRANE PROTEIN
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
Soluble cytochrome b562 / Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsJang HS
Funding support Korea, Republic Of, 3 items
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 CW / Jang HS / Woo JS
History
DepositionJul 11, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60777.png

Downloads & links

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Map

FileDownload / File: emd_60777.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 250 pix.
= 160. Å		0.64 Å/pix.
x 250 pix.
= 160. Å		0.64 Å/pix.
x 250 pix.
= 160. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.072673336 - 0.16041458
Average (Standard dev.)0.0016715893 (±0.008871984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 160.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60777_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60777_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Connexin36

EntireName: Connexin36
Components
  • Complex: Connexin36
    • Protein or peptide: Gap junction delta-2 protein,Soluble cytochrome b562
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: TETRADECANE

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Supramolecule #1: Connexin36

SupramoleculeName: Connexin36 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gap junction delta-2 protein,Soluble cytochrome b562

MacromoleculeName: Gap junction delta-2 protein,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.035426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGEWTILERL LEAAVQQHST MIGRILLTVV VIFRILIVAI VGETVYDDEQ TMFVCNTLQP GCNQACYDRA FPISHIRYWV FQIIMVCTP SLCFITYSVH QSAKQRERRA DLEDNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDAQ KATPPKLEDK S PDSPEMKD ...String:
MGEWTILERL LEAAVQQHST MIGRILLTVV VIFRILIVAI VGETVYDDEQ TMFVCNTLQP GCNQACYDRA FPISHIRYWV FQIIMVCTP SLCFITYSVH QSAKQRERRA DLEDNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDAQ KATPPKLEDK S PDSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQAA AEQLKTTRNA YIQKYLKLRR QEGISRFYII QVVFRNALEI GF LVGQYFL YGFSVPGLYE CNRYPCIKEV ECYVSRPTEK TVFLVFMFAV SGICVVLNLA ELNHLGWRKI KLAVRGAQAK RKS IYEIRN KDLPRVSVPN FGRTQSSDSA YVSRGDMLEV LFQ

UniProtKB: Gap junction delta-2 protein, Soluble cytochrome b562, Gap junction delta-2 protein

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Macromolecule #2: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 12 / Formula: MC3
Molecular weightTheoretical: 677.933 Da
Chemical component information

ChemComp-MC3:
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #3: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 3 / Number of copies: 6 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.54 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMKClPotassium chloride
2.0 mMC2H6OSbeta-mercaptoethanol

Details: 20mM HEPES(pH 7.5), 150mM KCl, 2mM beta-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5096 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 6001 / Average exposure time: 6.76 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1648256
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111066
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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