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- EMDB-60717: Consensus map of Cx43/GJA1 gap junction intercellular channel in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-60717
TitleConsensus map of Cx43/GJA1 gap junction intercellular channel in POPE nanodiscs, treated with a 5-fold molar excess of carbenoxolone (including D6 and D1 symmetry maps)
Map dataprimary map refined with D6 symmetry
Sample
  • Complex: connexin43
    • Protein or peptide: Connexin43
KeywordsGap junction / connexin43 / inhibitor / carbenoxolone / MEMBRANE PROTEIN
Function / homology
Function and homology information


gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / cell communication by electrical coupling / negative regulation of trophoblast cell migration / SARS-CoV-2 targets PDZ proteins in cell-cell junction / gap junction channel activity involved in cell communication by electrical coupling / microtubule-based transport / gap junction hemi-channel activity ...gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / cell communication by electrical coupling / negative regulation of trophoblast cell migration / SARS-CoV-2 targets PDZ proteins in cell-cell junction / gap junction channel activity involved in cell communication by electrical coupling / microtubule-based transport / gap junction hemi-channel activity / monoatomic ion transmembrane transporter activity / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / gap junction assembly / Regulation of gap junction activity / atrial cardiac muscle cell action potential / glutathione transmembrane transporter activity / cardiac conduction system development / connexin complex / cell-cell contact zone / cell communication by electrical coupling involved in cardiac conduction / Golgi-associated vesicle membrane / Formation of annular gap junctions / Gap junction degradation / gap junction / bone remodeling / Gap junction assembly / export across plasma membrane / gap junction channel activity / glutamate secretion / tight junction / xenobiotic transport / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of stem cell proliferation / maintenance of blood-brain barrier / RHOJ GTPase cycle / RHOQ GTPase cycle / establishment of mitotic spindle orientation / intercalated disc / efflux transmembrane transporter activity / alpha-tubulin binding / positive regulation of vascular associated smooth muscle cell proliferation / tubulin binding / negative regulation of cell growth / beta-catenin binding / bone development / cellular response to amyloid-beta / cell junction / intracellular protein localization / cell-cell signaling / positive regulation of cold-induced thermogenesis / heart development / monoatomic ion transmembrane transport / spermatogenesis / positive regulation of canonical NF-kappaB signal transduction / apical plasma membrane / membrane raft / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / positive regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily ...Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / 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 alpha-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsLee CW
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
History
DepositionJul 8, 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_60717.png

Downloads & links

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Map

FileDownload / File: emd_60717.map.gz / Format: CCP4 / Size: 244.1 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.)
1.14 Å/pix.
x 400 pix.
= 457.6 Å		1.14 Å/pix.
x 400 pix.
= 457.6 Å		1.14 Å/pix.
x 400 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-0.69661105 - 2.2299912
Average (Standard dev.)-0.00050228264 (±0.05682876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 457.60004 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_60717_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_60717_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_60717_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 : connexin43

EntireName: connexin43
Components
  • Complex: connexin43
    • Protein or peptide: Connexin43

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Supramolecule #1: connexin43

SupramoleculeName: connexin43 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: C-terminal truncated connexin43 gap junction intercellular channel is reconstituted into lipid nanodiscs with POPE and MSP protein.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Connexin43

MacromoleculeName: Connexin43 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDWSALGKL LDKVQAYSTA GGKVWLSVL FIFRILLLGT A VESAWGDE QSAFRCNTQQ PG CENVCYD KSFPISHVRF WVL QIIFVS VPTLLYLAHV FYVM RKEEK LNKKEEELKV AQTDG VNVD MHLKQIEIKK FKYGIE EHG KVKMRGGLLR TYIISIL FK ...String:
MGDWSALGKL LDKVQAYSTA GGKVWLSVL FIFRILLLGT A VESAWGDE QSAFRCNTQQ PG CENVCYD KSFPISHVRF WVL QIIFVS VPTLLYLAHV FYVM RKEEK LNKKEEELKV AQTDG VNVD MHLKQIEIKK FKYGIE EHG KVKMRGGLLR TYIISIL FK SIFEVAFLLI QWYIYGFS L SAVYTCKRDP CPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELF YVFFKGVKDR V KGKSDPYH ATSGALSPAS RG DMLEVLF Q

UniProtKB: Gap junction alpha-1 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

Concentration1.85 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMKClPotassium chloride
2.0 mMC2H6OSbeta-mercaptoethanol

Details: 20mM Tris(pH 8.0), 150mM KCl, 2mM beta-mercaptoethanol
GridModel: Quantifoil R2/1 / 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 GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 1449 / Average exposure time: 40.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 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: 2.25 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 92000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2055264
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: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46417
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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