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- EMDB-31495: Structure of connexin43/Cx43/GJA1 gap junction intercellular chan... -

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Basic information

Entry
Database: EMDB / ID: EMD-31495
TitleStructure of connexin43/Cx43/GJA1 gap junction intercellular channel in LMNG/CHS detergents at pH ~8.0
Map data
Sample
  • Complex: Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS)
    • Protein or peptide: Gap junction alpha-1 protein
  • Ligand: TETRADECANE
  • Ligand: water
KeywordsCx43 / Connexin / Gap junction channel / Gating mechanism / 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 / microtubule-based transport / gap junction channel activity involved in cell communication by electrical coupling / 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 / microtubule-based transport / gap junction channel activity involved in cell communication by electrical coupling / 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 / gap junction / Golgi-associated vesicle membrane / cell communication by electrical coupling involved in cardiac conduction / Formation of annular gap junctions / Gap junction degradation / gap junction channel activity / Gap junction assembly / bone remodeling / export across plasma membrane / glutamate secretion / tight junction / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / xenobiotic transport / 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 / 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 / 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: 3.1 Å
AuthorsLee HJ / Cha HJ
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2018R1C1B6004447 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2023
Title: Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM.
Authors: Hyuk-Joon Lee / Hyung Jin Cha / Hyeongseop Jeong / Seu-Na Lee / Chang-Won Lee / Minsoo Kim / Jejoong Yoo / Jae-Sung Woo /
Abstract: Connexin family proteins assemble into hexameric hemichannels in the cell membrane. The hemichannels dock together between two adjacent membranes to form gap junction intercellular channels (GJIChs). ...Connexin family proteins assemble into hexameric hemichannels in the cell membrane. The hemichannels dock together between two adjacent membranes to form gap junction intercellular channels (GJIChs). We report the cryo-electron microscopy structures of Cx43 GJICh, revealing the dynamic equilibrium state of various channel conformations in detergents and lipid nanodiscs. We identify three different N-terminal helix conformations of Cx43-gate-covering (GCN), pore-lining (PLN), and flexible intermediate (FIN)-that are randomly distributed in purified GJICh particles. The conformational equilibrium shifts to GCN by cholesteryl hemisuccinates and to PLN by C-terminal truncations and at varying pH. While GJIChs that mainly comprise GCN protomers are occluded by lipids, those containing conformationally heterogeneous protomers show markedly different pore sizes. We observe an α-to-π-helix transition in the first transmembrane helix, which creates a side opening to the membrane in the FIN and PLN conformations. This study provides basic structural information to understand the mechanisms of action and regulation of Cx43 GJICh.
History
DepositionJul 3, 2021-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31495.png

Downloads & links

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Map

FileDownload / File: emd_31495.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 400 pix.
= 270. Å		0.68 Å/pix.
x 400 pix.
= 270. Å		0.68 Å/pix.
x 400 pix.
= 270. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.13309298 - 0.2038235
Average (Standard dev.)0.00022232394 (±0.005786274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_31495_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_31495_half_map_2.map
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Sample components

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Entire : Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS)

EntireName: Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS)
Components
  • Complex: Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS)
    • Protein or peptide: Gap junction alpha-1 protein
  • Ligand: TETRADECANE
  • Ligand: water

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Supramolecule #1: Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS)

SupramoleculeName: Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Human Cx43 gap junction channel with gate-covering NTH conformation
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gap junction alpha-1 protein

MacromoleculeName: Gap junction alpha-1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.061336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPT LLYLAHVFYV MRKEEKLNKK EEELKVAQTD GVNVDMHLKQ IEIKKFKYGI EEHGKVKMRG GLLRTYIISI L FKSIFEVA ...String:
MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPT LLYLAHVFYV MRKEEKLNKK EEELKVAQTD GVNVDMHLKQ IEIKKFKYGI EEHGKVKMRG GLLRTYIISI L FKSIFEVA FLLIQWYIYG FSLSAVYTCK RDPCPHQVDC FLSRPTEKTI FIIFMLVVSL VSLALNIIEL FYVFFKGVKD RV KGKSDPY HATSGALSPA KDCGSQKYAY FNGCSSPTAP LSPMSPPGYK LVTGDRNNSS CRNYNKQASE QNWANYSAEQ NRM GQAGST ISNSHAQPFD FPDDNQNSKK LAAGHELQPL AIVDQRPSSR ASSRASSRPR PDDLEI

UniProtKB: Gap junction alpha-1 protein

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Macromolecule #2: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 2 / Number of copies: 132 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 264 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21689
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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