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- EMDB-54025: Tomogram of human connexin43 / GJC gap junction plaque -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54025
TitleTomogram of human connexin43 / GJC gap junction plaque
Map data
Sample
  • Cell: HEK293T cell
KeywordsCx43 / GJC / gap junction / cell signalling / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsEshriew E / Kumpula E-P / Teli S / Huiskonen JT
Funding support Finland, 1 items
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, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54025.png

Downloads & links

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Map

FileDownload / File: emd_54025.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.62 Å/pix.
x 512 pix.
= 4925.44 Å		9.62 Å/pix.
x 1024 pix.
= 9850.88 Å		9.62 Å/pix.
x 1024 pix.
= 9850.88 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 9.62 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.18945312 - 0.5214844
Average (Standard dev.)0.000000000218125 (±0.015913185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024512
Spacing10241024512
CellA: 9850.88 Å / B: 9850.88 Å / C: 4925.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HEK293T cell

EntireName: HEK293T cell
Components
  • Cell: HEK293T cell

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Supramolecule #1: HEK293T cell

SupramoleculeName: HEK293T cell / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statetissue

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.3 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 80 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 1 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: Warp (ver. 2.0.0) / Number images used: 53
CTF correctionSoftware - Name: Warp (ver. 2.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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Atomic model buiding 1

Initial modelPDB ID:

7z22


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient

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