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- EMDB-33391: Structure of connexin43/Cx43/GJA1 gap junction intercellular chan... -

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Basic information

Entry
Database: EMDB / ID: EMD-33391
TitleStructure of connexin43/Cx43/GJA1 gap junction intercellular channel in GDN detergents at pH ~8.0
Map datasharpened map
Sample
  • Complex: Dodecameric complex of human Cx43/GJA1 in detergents (GDN)
    • Protein or peptide: Gap junction alpha-1 protein
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 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 / regulation of bone remodeling / monoatomic ion transmembrane transporter activity / SARS-CoV-2 targets PDZ proteins in cell-cell junction / gap junction channel activity involved in cell communication by electrical coupling / contractile muscle fiber / regulation of ventricular cardiac muscle cell membrane depolarization / 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 / cellular response to pH / cardiac conduction system development / regulation of atrial cardiac muscle cell membrane depolarization / connexin complex / fascia adherens / Golgi-associated vesicle membrane / Formation of annular gap junctions / gap junction / cell-cell contact zone / Gap junction degradation / cell communication by electrical coupling involved in cardiac conduction / skeletal muscle tissue regeneration / bone remodeling / 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 / embryonic digit morphogenesis / maintenance of blood-brain barrier / positive regulation of stem cell proliferation / beta-tubulin binding / RHOJ GTPase cycle / heart looping / RHOQ GTPase cycle / 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 / neuron migration / negative regulation of cell growth / bone development / beta-catenin binding / cellular response to amyloid-beta / male gonad development / osteoblast differentiation / cell junction / protein localization / cell-cell signaling / positive regulation of cold-induced thermogenesis / heart development / scaffold protein binding / monoatomic ion transmembrane transport / spermatogenesis / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / apical plasma membrane / membrane raft / Golgi membrane / signaling receptor binding / negative regulation of gene expression / intracellular membrane-bounded organelle / focal adhesion / positive regulation of gene expression / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / nucleus / plasma membrane
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: 3.3 Å
AuthorsLee HJ / Cha HJ / Jeong H / Lee SN / Lee CW / Woo JS
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
DepositionMay 7, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33391.png

Downloads & links

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Map

FileDownload / File: emd_33391.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 256 pix.
= 292.864 Å		1.14 Å/pix.
x 256 pix.
= 292.864 Å		1.14 Å/pix.
x 256 pix.
= 292.864 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-2.225841 - 4.237896
Average (Standard dev.)0.0060011814 (±0.17453136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 292.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_33391_half_map_1.map
Annotationhalf map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map

Fileemd_33391_half_map_2.map
Annotationhalf map
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Sample components

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

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

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

SupramoleculeName: Dodecameric complex of human Cx43/GJA1 in detergents (GDN)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / 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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7f92

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32618
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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