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- PDB-8iyg: Human neuronal gap junction channel connexin 36 -

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Basic information

Entry
Database: PDB / ID: 8iyg
TitleHuman neuronal gap junction channel connexin 36
ComponentsGap junction delta-2 protein
KeywordsMEMBRANE PROTEIN / channel neuronal connexin dodecamer
Function / homology
Function and homology information


Electric Transmission Across Gap Junctions / connexin complex / gap junction channel activity / Gap junction assembly / neuronal action potential / visual perception / cell-cell signaling / chemical synaptic transmission / synapse / plasma membrane
Similarity search - Function
Gap junction delta-2 protein (Cx36) / 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
CHOLESTEROL HEMISUCCINATE / Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 2.69 Å
AuthorsMao, W.X. / Chen, S.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Arch Biochem Biophys / Year: 2024
Title: Assembly mechanisms of the neuronal gap junction channel connexin 36 elucidated by Cryo-EM.
Authors: Wenxuan Mao / Shanshuang Chen /
Abstract: Electrical synapses are essential components of neural circuits. Neuronal signal transduction across electrical synapses is primarily mediated by gap junction channels composed of Connexin36 (Cx36), ...Electrical synapses are essential components of neural circuits. Neuronal signal transduction across electrical synapses is primarily mediated by gap junction channels composed of Connexin36 (Cx36), the lack of which causes impaired electrical coupling between certain neurons including cortical interneurons and thalamic reticular nucleus (TRN) neurons. However, the structural basis underlying Cx36 function and assembly remains elusive. Recently, Lee et al. reported cryo-EM structures of Cx36, thus provided first insights of its gating mechanism. Here, we report a consistent cryo-EM structure of Cx36 determined in parallel, and describe unique interactions underpinning its assembly mechanism in complementary to the competing work. In particular, we found non-canonical electrostatic interactions between protomers from opposing hemichannels and a steric complementary site between adjacent protomers within a hemichannel, which together provide a structural explanation for the assembly specificity in homomeric and heteromeric gap junction channels.
History
DepositionApr 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 10, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Apr 10, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 10, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 16, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gap junction delta-2 protein
B: Gap junction delta-2 protein
C: Gap junction delta-2 protein
D: Gap junction delta-2 protein
E: Gap junction delta-2 protein
F: Gap junction delta-2 protein
G: Gap junction delta-2 protein
H: Gap junction delta-2 protein
I: Gap junction delta-2 protein
J: Gap junction delta-2 protein
K: Gap junction delta-2 protein
L: Gap junction delta-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,883144
Polymers433,62812
Non-polymers66,255132
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Gap junction delta-2 protein / Connexin-36 / Cx36 / Gap junction alpha-9 protein


Mass: 36135.672 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GJD2, GJA9 / Production host: eukaryotic plasmids (others) / References: UniProt: Q9UKL4
#2: Chemical...
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 84 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
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: human neuronal gap junction channel connexin 36 / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117469 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00121024
ELECTRON MICROSCOPYf_angle_d0.35228476
ELECTRON MICROSCOPYf_dihedral_angle_d4.1963468
ELECTRON MICROSCOPYf_chiral_restr0.0333396
ELECTRON MICROSCOPYf_plane_restr0.0023144

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