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- EMDB-38221: Consensus map of Cx43/GJA1 gap junction channel in the presence o... -

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Basic information

Entry
Database: EMDB / ID: EMD-38221
TitleConsensus map of Cx43/GJA1 gap junction channel in the presence of diC8-PIP2 (16-fold molar excess)
Map dataFull map
Sample
  • Organelle or cellular component: Dodecameric complex of human Cx43-M257 in lipid nanodiscs (POPE) in the presence of diC8-PIP2 (16-fold molar excess)
    • Protein or peptide: A C-terminal truncated mutant of gap junction alpha-1 protein (Cx43-M257)
KeywordsCx43 gap junction channel / PIP2 / Cytoplasmic loop / Opening / 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 / gap junction hemi-channel activity / SARS-CoV-2 targets PDZ proteins in cell-cell junction / microtubule-based transport / gap junction channel activity involved in cell communication by electrical coupling ...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 / gap junction hemi-channel activity / SARS-CoV-2 targets PDZ proteins in cell-cell junction / microtubule-based transport / gap junction channel activity involved in cell communication by electrical coupling / monoatomic ion transmembrane transporter activity / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / glutathione transmembrane transporter activity / 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 / cardiac conduction system development / connexin complex / gap junction / Formation of annular gap junctions / cell-cell contact zone / Golgi-associated vesicle membrane / cell communication by electrical coupling involved in cardiac conduction / Gap junction degradation / bone remodeling / Gap junction assembly / gap junction channel activity / export across plasma membrane / glutamate secretion / tight junction / xenobiotic transport / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / maintenance of blood-brain barrier / positive regulation of stem cell proliferation / 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 / bone development / beta-catenin binding / 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 / endoplasmic reticulum membrane / positive regulation of gene expression / 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: 3.0 Å
AuthorsLee HJ / Cha HJ / Woo JS
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
Other privateSUHF-18010097
National Research Foundation (NRF, Korea)RS-2023-00217798 Korea, Republic Of
CitationJournal: To Be Published
Title: PIP2-dependent conformational changes and stabilization of cytoplasmic loop in Cx43/GJA1 gap junction channel
Authors: Lee HJ / Cha HJ / Woo JS
History
DepositionDec 6, 2023-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_38221.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Voxel sizeX=Y=Z: 0.8943 Å
Density
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-0.8461341 - 1.6273937
Average (Standard dev.)-0.0010086875 (±0.070091605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 321.948 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Dodecameric complex of human Cx43-M257 in lipid nanodiscs (POPE) ...

EntireName: Dodecameric complex of human Cx43-M257 in lipid nanodiscs (POPE) in the presence of diC8-PIP2 (16-fold molar excess)
Components
  • Organelle or cellular component: Dodecameric complex of human Cx43-M257 in lipid nanodiscs (POPE) in the presence of diC8-PIP2 (16-fold molar excess)
    • Protein or peptide: A C-terminal truncated mutant of gap junction alpha-1 protein (Cx43-M257)

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Supramolecule #1: Dodecameric complex of human Cx43-M257 in lipid nanodiscs (POPE) ...

SupramoleculeName: Dodecameric complex of human Cx43-M257 in lipid nanodiscs (POPE) in the presence of diC8-PIP2 (16-fold molar excess)
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Human Cx43-M257 gap junction channel with mixed flexible-intermediate NTH (FIN) and pore-lining NTH (PLN) conformations
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: A C-terminal truncated mutant of gap junction alpha-1 protein (Cx...

MacromoleculeName: A C-terminal truncated mutant of gap junction alpha-1 protein (Cx43-M257)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL ...String:
MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL LIQWYIYGFS LSAVYTCKRD PCPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELFY VFFKGVKDRV KGKSDPYHAT SGALSPA

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

Concentration3.9 mg/mL
BufferpH: 8
GridMaterial: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

38220

Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5720
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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