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- PDB-8xbm: Structure of Cx43/GJA1 gap junction intercellular channel in comp... -

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Basic information

Entry
Database: PDB / ID: 8xbm
TitleStructure of Cx43/GJA1 gap junction intercellular channel in complex with diC8-PIP2
ComponentsGap junction alpha-1 protein
KeywordsMEMBRANE PROTEIN / Cx43 gap junction channel / PIP2 / Cytoplasmic loop / Opening
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 / cell communication by electrical coupling involved in cardiac conduction / gap junction / Golgi-associated vesicle membrane / 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
Chem-PIO / Gap junction alpha-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLee, H.J. / Cha, H.J. / Woo, J.S.
Funding support Korea, Republic Of, 2items
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, H.J. / Cha, H.J. / Woo, J.S.
History
DepositionDec 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,45524
Polymers351,49712
Non-polymers8,95912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 29291.387 Da / Num. of mol.: 12 / Fragment: C-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GJA1, GJAL / Production host: Homo sapiens (human) / References: UniProt: P17302
#2: Chemical
ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
Details: Human Cx43-M257 gap junction channel in complex with diC8-PIP2 (16-fold molar excess) with pore-lining NTH (PLN) conformation
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 3.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4412 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00223424
ELECTRON MICROSCOPYf_angle_d0.44531620
ELECTRON MICROSCOPYf_dihedral_angle_d10.8588664
ELECTRON MICROSCOPYf_chiral_restr0.0343576
ELECTRON MICROSCOPYf_plane_restr0.0023744

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