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- EMDB-60763: Consensus map of Cx36/GJD2 gap junction intercellular channel in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-60763
TitleConsensus map of Cx36/GJD2 gap junction intercellular channel in soybean polar lipid nanodiscs, treated with a 10-fold molar excess of carbenoxolone and incubated shortly (including D6 and D1 symmetry maps)
Map dataprimary map refined with D6 symmetry
Sample
  • Complex: Connexin36
    • Protein or peptide: Connexin36
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 / cell-cell signaling / chemical synaptic transmission / 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 channel protein cysteine-rich domain
Similarity search - Domain/homology
Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.04 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 10, 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_60763.png

Downloads & links

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Map

FileDownload / File: emd_60763.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map refined with D6 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 480 pix.
= 388.8 Å		0.81 Å/pix.
x 480 pix.
= 388.8 Å		0.81 Å/pix.
x 480 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.30285057 - 0.6711955
Average (Standard dev.)-0.00015821027 (±0.013827913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 388.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: the map refined with D1 symmetry, using same particles to D6 map

Fileemd_60763_additional_1.map
Annotationthe map refined with D1 symmetry, using same particles to D6 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map of primary map

Fileemd_60763_half_map_1.map
Annotationhalf-map of primary map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map of primary map

Fileemd_60763_half_map_2.map
Annotationhalf-map of primary 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: Connexin36

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Supramolecule #1: Connexin36

SupramoleculeName: Connexin36 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 10-fold molar excess to Cx36 protomer. Sample was incubated for 1 min before grid loading.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Connexin36

MacromoleculeName: Connexin36 / type: protein_or_peptide / ID: 1
Details: The human Cx36-BRIL proteins were expressed as fusion constructs with a human rhinovirus (HRV) 3C cleavage site, an enhanced yellow fluorescence protein (eYFP) tag, a 10xHis-tag and a rho- ...Details: The human Cx36-BRIL proteins were expressed as fusion constructs with a human rhinovirus (HRV) 3C cleavage site, an enhanced yellow fluorescence protein (eYFP) tag, a 10xHis-tag and a rho-1D4 epitope tag (8 amino acid sequence of TETSQVAPA) at its C-terminus.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGEWTILERL LEAAVQQHST MIGRILLTV VVIFRILIVA I VGETVYDD EQTMFVCNTL QP GCNQACY DRAFPISHIR YWV FQIIMV CTPSLCFITY SVHQ SAKQR ERRADLEDNW ETLND NLKV IEKADNAAQV KDALTK MRA AALDAQKATP PKLEDKS PD ...String:
MGEWTILERL LEAAVQQHST MIGRILLTV VVIFRILIVA I VGETVYDD EQTMFVCNTL QP GCNQACY DRAFPISHIR YWV FQIIMV CTPSLCFITY SVHQ SAKQR ERRADLEDNW ETLND NLKV IEKADNAAQV KDALTK MRA AALDAQKATP PKLEDKS PD SPEMKDFRHG FDILVGQI D DALKLANEGK VKEAQAAAE QLKTTRNAYI QKYLKLRRQE GISRFYIIQ VVFRNALEIG F LVGQYFLY GFSVPGLYEC NR YPCIKEV ECYVSRPTEK TVF LVFMFA VSGICVVLNL AELN HLGWR KIKLAVRGAQ AKRKS IYEI RNKDLPRVSV PNFGRT QSS DSAYVSRGDM LEVLFQ

UniProtKB: Gap junction delta-2 protein

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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

Concentration3.0 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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 5001 / Average exposure time: 6.79 sec. / Average electron dose: 50.0 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 / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 96000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2151580
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 246600
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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