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- PDB-9rkx: Atomic model of Cx43 gap junction channel rigid-body fitted to th... -

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Basic information

Entry
Database: PDB / ID: 9rkx
TitleAtomic model of Cx43 gap junction channel rigid-body fitted to the in situ structure of the human Cx43 gap junction
ComponentsGap junction alpha-1 protein
KeywordsMEMBRANE PROTEIN / Cx43 / GJC / gap junction / cell signalling
Function / homology
Function and homology information


gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / microtubule-based transport / 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 / monoatomic ion transmembrane transporter activity ...gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / microtubule-based transport / 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 / monoatomic ion transmembrane transporter activity / gap junction hemi-channel activity / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / Regulation of gap junction activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / glutathione transmembrane transporter activity / atrial cardiac muscle cell action potential / cardiac conduction system development / cell-cell contact zone / Golgi-associated vesicle membrane / connexin complex / cell communication by electrical coupling involved in cardiac conduction / Formation of annular gap junctions / Gap junction degradation / gap junction / bone remodeling / export across plasma membrane / Gap junction assembly / gap junction channel activity / glutamate secretion / tight junction / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of stem cell proliferation / RHOJ GTPase cycle / RHOQ GTPase cycle / establishment of mitotic spindle orientation / maintenance of blood-brain barrier / efflux transmembrane transporter activity / intercalated disc / xenobiotic transport / 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 / spermatogenesis / monoatomic ion transmembrane transport / positive regulation of canonical NF-kappaB signal transduction / apical plasma membrane / membrane raft / Golgi membrane / focal adhesion / 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)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 14 Å
AuthorsEshriew, E. / Kumpula, E.-P. / Teli, S. / Huiskonen, J.T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: Sci Adv / Year: 2026
Title: In situ structure of the human gap junction.
Authors: Evans Eshriew / Esa-Pekka Kumpula / Shiv K Sah-Teli / Amiel Abettan / Amina Djurabekova / Vivek Sharma / Juha T Huiskonen /
Abstract: Gap junction plaques (GJPs) enable direct intercellular communication and consist of connexin channels arranged into two-dimensional lattices. While structures of purified connexin channels have ...Gap junction plaques (GJPs) enable direct intercellular communication and consist of connexin channels arranged into two-dimensional lattices. While structures of purified connexin channels have informed models of gating, they omit key intracellular regions and lack native context. Here, we use cryo-electron tomography and focused ion beam milling to determine the in situ structure of human connexin 43 (Cx43) GJPs in HEK293 cells at 14-Å resolution. We reveal a previously unresolved structural contribution of the large carboxyl-terminal domain to lateral channel-channel interactions that appear critical for plaque assembly. Coarse-grained molecular dynamics simulations suggest how lipids and cholesterol occupy the space between adjacent connexins. These findings resolve a decades-old question regarding gap junction organization and highlight a mechanistic function for the carboxyl-terminal domain, likely regulated by a helix-loop-helix motif. Our study provides a structural blueprint for understanding how connexin diversity and regulation shape tissue-level communication in health and disease.
History
DepositionJun 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
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Revision 1.1May 27, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1May 27, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gap junction alpha-1 protein
B: Gap junction alpha-1 protein
C: Gap junction alpha-1 protein
D: Gap junction alpha-1 protein
E: Gap junction alpha-1 protein
F: Gap junction alpha-1 protein
G: Gap junction alpha-1 protein
H: Gap junction alpha-1 protein
I: Gap junction alpha-1 protein
J: Gap junction alpha-1 protein
K: Gap junction alpha-1 protein
L: Gap junction alpha-1 protein


Theoretical massNumber of molelcules
Total (without water)516,73612
Polymers516,73612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Gap junction alpha-1 protein / Connexin-43 / Cx43 / Gap junction 43 kDa heart protein


Mass: 43061.336 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GJA1, GJAL / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P17302
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: HEK293T cell / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 3000 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 160 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 1

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Processing

EM software
IDNameCategory
7UCSF ChimeraXmodel fitting
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11904 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 26 / Num. of volumes extracted: 50804
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 7z22

7z22


Accession code: 7z22 / Source name: PDB / Type: experimental model

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