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- EMDB-53250: Connexin-32 (Cx32) in MSP2N2 nanodiscs with liver polar lipids -

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Basic information

Entry
Database: EMDB / ID: EMD-53250
TitleConnexin-32 (Cx32) in MSP2N2 nanodiscs with liver polar lipids
Map dataConnexin-32 (Cx32) gap junction channel in MSP2N2 nanodiscs with liver polar lipids
Sample
  • Complex: Connexin-32 (Cx32) gap junction channel in MSP2N2 nanodiscs with liver polar lipids
    • Protein or peptide: Gap junction beta-1 protein,Green fluorescent protein
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
KeywordsGap junction channel / membrane transport / lipids / 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 / bioluminescence / generation of precursor metabolites and energy / nervous system development / cell-cell signaling ...Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / Gap junction assembly / gap junction channel activity / bioluminescence / generation of precursor metabolites and energy / 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 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Gap junction beta-1 protein / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 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 25, 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_53250.png

Downloads & links

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Map

FileDownload / File: emd_53250.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConnexin-32 (Cx32) gap junction channel in MSP2N2 nanodiscs with liver polar lipids
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 249.84 Å		0.65 Å/pix.
x 384 pix.
= 249.84 Å		0.65 Å/pix.
x 384 pix.
= 249.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0022
Minimum - Maximum-0.011497683 - 0.020597639
Average (Standard dev.)0.00008363877 (±0.00070853805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 249.84033 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53250_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: half-map 1

Fileemd_53250_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_53250_half_map_2.map
Annotationhalf-map 2
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Sample components

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Entire : Connexin-32 (Cx32) gap junction channel in MSP2N2 nanodiscs with ...

EntireName: Connexin-32 (Cx32) gap junction channel in MSP2N2 nanodiscs with liver polar lipids
Components
  • Complex: Connexin-32 (Cx32) gap junction channel in MSP2N2 nanodiscs with liver polar lipids
    • Protein or peptide: Gap junction beta-1 protein,Green fluorescent protein
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL

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Supramolecule #1: Connexin-32 (Cx32) gap junction channel in MSP2N2 nanodiscs with ...

SupramoleculeName: Connexin-32 (Cx32) gap junction channel in MSP2N2 nanodiscs with liver polar lipids
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gap junction beta-1 protein,Green fluorescent protein

MacromoleculeName: Gap junction beta-1 protein,Green fluorescent protein / type: protein_or_peptide / ID: 1
Details: Cx32 with a C-terminal 3C-YFP-twinStrep tag,Cx32 with a C-terminal 3C-YFP-twinStrep tag
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 63.327422 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 DRCSACAAAL EVLFQGPGGV SKGEELFTGV VPILVELDGD VNG HKFSVS GEGEGDATYG KLTLKFICTT GKLPVPWPTL VTTFGYGLQC FARYPDHMKQ HDFFKSAMPE GYVQERTIFF KDDG NYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNYNSHN VYIMADKQKN GIKVNFKIRH NIEDGSVQLA DHYQQ NTPI GDGPVLLPDN HYLSYQSALS KDPNEKRDHM VLLEFVTAAG ITLGMDELYK AASAWSHPQF EKGGGSGGGS GGSAWS HPQ FEK

UniProtKB: Gap junction beta-1 protein, Green fluorescent protein

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 12 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 12 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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
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 correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

15010

Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 53450
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationSoftware - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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