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- EMDB-53240: Connexin-32 (Cx32) gap junction channel in POPC-containing nanodi... -

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Basic information

Entry
Database: EMDB / ID: EMD-53240
TitleConnexin-32 (Cx32) gap junction channel in POPC-containing nanodiscs in the absence of CHS
Map dataPostprocessed map of Cx32 in nanodisc with POPC, in the absence of CHS
Sample
  • Complex: A dodecameric complex of connexin-32 (Cx32)
    • Protein or peptide: Gap junction beta-1 protein
KeywordsIon channel / gap junction / membrane transport / MEMBRANE PROTEIN
Function / homology
Function and homology information


Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / Gap junction assembly / gap junction channel activity / nervous system development / cell-cell signaling / endoplasmic reticulum membrane / identical protein binding
Similarity search - Function
Gap junction beta-1 protein (Cx32) / 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 beta-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsKorkhov VM / Lavriha P
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation184951 Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Lipid dependence of connexin-32 gap junction channel conformations.
Authors: Pia Lavriha / Carina Fluri / Jorge Enrique Hernández González / Volodymyr M Korkhov /
Abstract: Connexin-32 (Cx32) gap junction channels (GJCs) mediate intercellular coupling in various tissues, including myelinating Schwann cells. Mutations in Cx32, such as W3S, are associated with X-linked ...Connexin-32 (Cx32) gap junction channels (GJCs) mediate intercellular coupling in various tissues, including myelinating Schwann cells. Mutations in Cx32, such as W3S, are associated with X-linked Charcot-Marie-Tooth (CMT1X) disease. Lipids regulate Cx32 GJC permeation, although the regulatory mechanism is unclear. Here, we determine the cryo-EM structures of Cx32 GJCs reconstituted in nanodiscs, revealing that phospholipids block the Cx32 GJC pore by binding to the site formed by N-terminal gating helices. The phospholipid-bound state is contingent on the presence of a sterol molecule in a hydrophobic pocket formed by the N-terminus: the N-terminal helix of Cx32 fails to sustain a phospholipid binding site in the absence of cholesterol hemisuccinate. The CMT1X-linked W3S mutant which has an impaired sterol binding site adopts a conformation of the N-terminus incompatible with phospholipid binding. Our results indicate that different lipid species control connexin channel gating directly by influencing the conformation of the N-terminal gating helix.
History
DepositionMar 24, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53240.png

Downloads & links

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Map

FileDownload / File: emd_53240.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of Cx32 in nanodisc with POPC, in the absence of CHS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 249.99 Å		0.65 Å/pix.
x 384 pix.
= 249.99 Å		0.65 Å/pix.
x 384 pix.
= 249.99 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65101 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0014
Minimum - Maximum-0.0057484605 - 0.0111389365
Average (Standard dev.)0.0000655139 (±0.00042243712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 249.98972 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53240_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_53240_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_53240_half_map_2.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A dodecameric complex of connexin-32 (Cx32)

EntireName: A dodecameric complex of connexin-32 (Cx32)
Components
  • Complex: A dodecameric complex of connexin-32 (Cx32)
    • Protein or peptide: Gap junction beta-1 protein

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Supramolecule #1: A dodecameric complex of connexin-32 (Cx32)

SupramoleculeName: A dodecameric complex of connexin-32 (Cx32) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gap junction beta-1 protein

MacromoleculeName: Gap junction beta-1 protein / type: protein_or_peptide / ID: 1
Details: human Cx32 with a C-terminal 3C protease cleavage site, YFP and twinStrep tag.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.065533 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNWTGLYTLL SGVNRHSTAI GRVWLSVIFI FRIMVLVVAA ESVWGDEKSS FICNTLQPGC NSVCYDQFFP ISHVRLWSLQ LILVSTPAL LVAMHVAHQQ HIEKKMLRLE GHGDPLHLEE VKRHKVHISG TLWWTYVISV VFRLLFEAVF MYVFYLLYPG Y AMVRLVKC ...String:
MNWTGLYTLL SGVNRHSTAI GRVWLSVIFI FRIMVLVVAA ESVWGDEKSS FICNTLQPGC NSVCYDQFFP ISHVRLWSLQ LILVSTPAL LVAMHVAHQQ HIEKKMLRLE GHGDPLHLEE VKRHKVHISG TLWWTYVISV VFRLLFEAVF MYVFYLLYPG Y AMVRLVKC DVYPCPNTVD CFVSRPTEKT VFTVFMLAAS GICIILNVAE VVYLIIRACA RRAQRRSNPP SRKGSGFGHR LS PEYKQNE INKLLSEQDG SLKDILRRSP GTGAGLAEKS DRCSAC

UniProtKB: Gap junction beta-1 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
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: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

15010

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15537
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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