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- EMDB-54525: in situ Gap Junction C. elegans Class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-54525
Titlein situ Gap Junction C. elegans Class 2
Map data
Sample
  • Complex: in situ Gap Junction C. elegans
Keywordsin situ Gap Junction ion transfer cellular communication electrical synapse cell-cell contact / MEMBRANE PROTEIN
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsubtomogram averaging / cryo EM / Resolution: 18.0 Å
AuthorsRosenkranz N / Gottschalk A
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Sci Adv / Year: 2025
Title: In situ structure of a gap junction-stomatin complex.
Authors: Nils Rosenkranz / Alexandra N Birtasu / Konstantin Wieland / Lisa Rehm / Rachita Sharma / Atal Vats / Sina Manger / Aayush Srivastava / Abhishek Bhattacharya / Gerhard Hummer / Achilleas S ...Authors: Nils Rosenkranz / Alexandra N Birtasu / Konstantin Wieland / Lisa Rehm / Rachita Sharma / Atal Vats / Sina Manger / Aayush Srivastava / Abhishek Bhattacharya / Gerhard Hummer / Achilleas S Frangakis / Alexander Gottschalk /
Abstract: Gap junctions (GJs) are intercellular channels that mediate electrical signals and transfer of small molecules. They are crucial for brain, heart, and other organ functions. While molecular ...Gap junctions (GJs) are intercellular channels that mediate electrical signals and transfer of small molecules. They are crucial for brain, heart, and other organ functions. While molecular structures of purified homomeric GJs are available, information of in situ structures is lacking. In vivo, GJs can form heteromers with different functionalities and may associate with other proteins. Here, we analyzed GJs by cryo-electron tomography and subtomogram averaging. We observed hexagonal arrays of GJs at cellular junctions in primary embryonal cells that displayed distinct wide and narrow conformations. Moreover, we found a cap-like, cytosolic protein assembly enclosing the channel pore. We propose that the cap is formed by the stomatin UNC-1, known to interact with UNC-9 innexins. This is corroborated by matching AlphaFold3 models of UNC-1 multimers with our subtomogram average structure; by expressing GFP-tagged UNC-1, leading to cap structures with additional density; and by coarse-grained MD simulations. UNC-1/stomatin rings may affect GJ formation or functions, possibly beyond nematodes.
History
DepositionJul 23, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54525.png

Downloads & links

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Map

FileDownload / File: emd_54525.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.58 Å/pix.
x 96 pix.
= 247.219 Å		2.58 Å/pix.
x 96 pix.
= 247.219 Å		2.58 Å/pix.
x 96 pix.
= 247.219 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5752 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0101
Minimum - Maximum-0.018234987 - 0.028856896
Average (Standard dev.)0.004172713 (±0.0056365207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 247.21921 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54525_msk_1.map
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Half map: #1

Fileemd_54525_half_map_1.map
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Half map: #2

Fileemd_54525_half_map_2.map
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Sample components

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Entire : in situ Gap Junction C. elegans

EntireName: in situ Gap Junction C. elegans
Components
  • Complex: in situ Gap Junction C. elegans

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Supramolecule #1: in situ Gap Junction C. elegans

SupramoleculeName: in situ Gap Junction C. elegans / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 1281
ExtractionNumber tomograms: 66 / Number images used: 9206 / Software - Name: RELION
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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