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- EMDB-15011: cryo-EM structure of Connexin 32 gap junction channel -

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Basic information

Entry
Database: EMDB / ID: EMD-15011
Titlecryo-EM structure of Connexin 32 gap junction channel
Map data
Sample
  • Complex: Connexin32 gap junction channel complex
    • Protein or peptide: Gap junction beta-1 protein
  • Ligand: CHOLESTEROL
Keywordsconnexin / Hemi channel / cell communication / MEMBRANE PROTEIN
Function / homology
Function and homology information


purine ribonucleotide transport / epididymis development / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / Gap junction assembly / gap junction channel activity / lateral plasma membrane / cell-cell signaling ...purine ribonucleotide transport / epididymis development / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / Gap junction assembly / gap junction channel activity / lateral plasma membrane / cell-cell signaling / nervous system development / 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: 3.06 Å
AuthorsQi C / Korkhov VM
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation184951 Switzerland
CitationJournal: Sci Adv / Year: 2023
Title: Structures of wild-type and selected CMT1X mutant connexin 32 gap junction channels and hemichannels.
Authors: Chao Qi / Pia Lavriha / Erva Bayraktar / Anand Vaithia / Dina Schuster / Micaela Pannella / Valentina Sala / Paola Picotti / Mario Bortolozzi / Volodymyr M Korkhov /
Abstract: In myelinating Schwann cells, connection between myelin layers is mediated by gap junction channels (GJCs) formed by docked connexin 32 (Cx32) hemichannels (HCs). Mutations in Cx32 cause the X-linked ...In myelinating Schwann cells, connection between myelin layers is mediated by gap junction channels (GJCs) formed by docked connexin 32 (Cx32) hemichannels (HCs). Mutations in Cx32 cause the X-linked Charcot-Marie-Tooth disease (CMT1X), a degenerative neuropathy without a cure. A molecular link between Cx32 dysfunction and CMT1X pathogenesis is still missing. Here, we describe the high-resolution cryo-electron cryo-myography (cryo-EM) structures of the Cx32 GJC and HC, along with two CMT1X-linked mutants, W3S and R22G. While the structures of wild-type and mutant GJCs are virtually identical, the HCs show a major difference: In the W3S and R22G mutant HCs, the amino-terminal gating helix partially occludes the pore, consistent with a diminished HC activity. Our results suggest that HC dysfunction may be involved in the pathogenesis of CMT1X.
History
DepositionMay 21, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15011.png

Downloads & links

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Map

FileDownload / File: emd_15011.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.654 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.044485226 - 0.07232738
Average (Standard dev.)0.00018928961 (±0.0019746171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 251.13599 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15011_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15011_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15011_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Connexin32 gap junction channel complex

EntireName: Connexin32 gap junction channel complex
Components
  • Complex: Connexin32 gap junction channel complex
    • Protein or peptide: Gap junction beta-1 protein
  • Ligand: CHOLESTEROL

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Supramolecule #1: Connexin32 gap junction channel complex

SupramoleculeName: Connexin32 gap junction channel complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32 kDa/nm

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Macromolecule #1: Gap junction beta-1 protein

MacromoleculeName: Gap junction beta-1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97151
FSC plot (resolution estimation)

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