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- EMDB-35821: Human neuronal gap junction channel connexin 36 -

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Basic information

Entry
Database: EMDB / ID: EMD-35821
TitleHuman neuronal gap junction channel connexin 36
Map data
Sample
  • Complex: human neuronal gap junction channel connexin 36
    • Protein or peptide: Gap junction delta-2 protein
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
Keywordschannel neuronal connexin dodecamer / MEMBRANE PROTEIN
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
Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / Resolution: 2.69 Å
AuthorsMao WX / Chen SS
Funding support China, 1 items
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, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35821.png

Downloads & links

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Map

FileDownload / File: emd_35821.map.gz / Format: CCP4 / Size: 83.7 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.)
1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.158
Minimum - Maximum-0.30655256 - 0.80944973
Average (Standard dev.)0.001201687 (±0.027111743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35821_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35821_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : human neuronal gap junction channel connexin 36

EntireName: human neuronal gap junction channel connexin 36
Components
  • Complex: human neuronal gap junction channel connexin 36
    • Protein or peptide: Gap junction delta-2 protein
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: human neuronal gap junction channel connexin 36

SupramoleculeName: human neuronal gap junction channel connexin 36 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gap junction delta-2 protein

MacromoleculeName: Gap junction delta-2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.135672 KDa
Recombinant expressionOrganism: eukaryotic plasmids (others)
SequenceString: MGEWTILERL LEAAVQQHST MIGRILLTVV VIFRILIVAI VGETVYDDEQ TMFVCNTLQP GCNQACYDRA FPISHIRYWV FQIIMVCTP SLCFITYSVH QSAKQRERRY STVFLALDRD PPESIGGPGG TGGGGSGGGK REDKKLQNAI VNGVLQNTEN T SKETEPDC ...String:
MGEWTILERL LEAAVQQHST MIGRILLTVV VIFRILIVAI VGETVYDDEQ TMFVCNTLQP GCNQACYDRA FPISHIRYWV FQIIMVCTP SLCFITYSVH QSAKQRERRY STVFLALDRD PPESIGGPGG TGGGGSGGGK REDKKLQNAI VNGVLQNTEN T SKETEPDC LEVKELTPHP SGLRTASKSK LRRQEGISRF YIIQVVFRNA LEIGFLVGQY FLYGFSVPGL YECNRYPCIK EV ECYVSRP TEKTVFLVFM FAVSGICVVL NLAELNHLGW RKIKLAVRGA QAKRKSIYEI RNKDLPRVSV PNFGRTQSSD SAY V

UniProtKB: Gap junction delta-2 protein

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 48 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 3 / Number of copies: 84 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117469
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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