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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 striated muscle tissue development / milk ejection reflex / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / neuroblast migration ...gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / positive regulation of striated muscle tissue development / milk ejection reflex / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / neuroblast migration / columnar/cuboidal epithelial cell maturation / negative regulation of trophoblast cell migration / microtubule-based transport / gap junction hemi-channel activity / monoatomic ion transmembrane transporter activity / regulation of bone remodeling / SARS-CoV-2 targets PDZ proteins in cell-cell junction / gap junction channel activity involved in cell communication by electrical coupling / regulation of ventricular cardiac muscle cell membrane depolarization / contractile muscle fiber / 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 / atrial cardiac muscle cell action potential / Regulation of gap junction activity / cardiac conduction system development / regulation of atrial cardiac muscle cell membrane depolarization / cellular response to pH / connexin complex / fascia adherens / gap junction / cell-cell contact zone / Formation of annular gap junctions / Golgi-associated vesicle membrane / cell communication by electrical coupling involved in cardiac conduction / Gap junction degradation / bone remodeling / skeletal muscle tissue regeneration / gap junction channel activity / Gap junction assembly / regulation of bone mineralization / export across plasma membrane / adult heart development / regulation of ventricular cardiac muscle cell membrane repolarization / tight junction / glutamate secretion / blood vessel morphogenesis / lens development in camera-type eye / intermediate filament / xenobiotic transport / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / embryonic digit morphogenesis / maintenance of blood-brain barrier / positive regulation of stem cell proliferation / beta-tubulin binding / RHOJ GTPase cycle / RHOQ GTPase cycle / heart looping / establishment of mitotic spindle orientation / efflux transmembrane transporter activity / intercalated disc / alpha-tubulin binding / lateral plasma membrane / T cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / tubulin binding / protein tyrosine kinase binding / negative regulation of cell growth / beta-catenin binding / bone development / cellular response to amyloid-beta / male gonad development / neuron migration / osteoblast differentiation / cell junction / intracellular protein localization / cell-cell signaling / positive regulation of cold-induced thermogenesis / heart development / scaffold protein binding / monoatomic ion transmembrane transport / spermatogenesis / in utero embryonic development / positive regulation of canonical NF-kappaB signal transduction / apical plasma membrane / membrane raft / Golgi membrane / signaling receptor binding / negative regulation of gene expression / focal adhesion / intracellular membrane-bounded organelle / positive regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / nucleus
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

Supplemental images

emd_38221.png

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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 321.948 Å		0.89 Å/pix.
x 360 pix.
= 321.948 Å		0.89 Å/pix.
x 360 pix.
= 321.948 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8943 Å
Density

Histogram

Histogram (log scale)
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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Additional map: C1 processed map of the full map

Fileemd_38221_additional_1.map
AnnotationC1 processed map of the full map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_38221_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_38221_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
FSC plot (resolution estimation)

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