[English] 日本語
Yorodumi
- EMDB-53244: Connexin-32 (Cx32) W3S mutant gap junction channel in POPC-contai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53244
TitleConnexin-32 (Cx32) W3S mutant gap junction channel in POPC-containing MSP2N2 nanodiscs
Map dataPostprocessed map of connexin-32 (Cx32) W3S mutant in POPC-containing MSP2N2 nanodiscs
Sample
  • Complex: A dodecameric complex of connexin-32 (Cx32) W3S mutant gap junction channel
    • Protein or peptide: Gap junction beta-1 protein,Gap junction beta-1 protein,Green fluorescent 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) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsKorkhov VM / Lavriha P / Fluri C
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

-
Structure visualization

Supplemental images

emd_53244.png

Downloads & links

-
Map

FileDownload / File: emd_53244.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of connexin-32 (Cx32) W3S mutant in POPC-containing MSP2N2 nanodiscs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 253.777 Å		0.66 Å/pix.
x 384 pix.
= 253.777 Å		0.66 Å/pix.
x 384 pix.
= 253.777 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.0077667125 - 0.019761927
Average (Standard dev.)0.000087903034 (±0.00066525885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 253.77744 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53244_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map 1

Fileemd_53244_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map 2

Fileemd_53244_half_map_2.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A dodecameric complex of connexin-32 (Cx32) W3S mutant gap juncti...

EntireName: A dodecameric complex of connexin-32 (Cx32) W3S mutant gap junction channel
Components
  • Complex: A dodecameric complex of connexin-32 (Cx32) W3S mutant gap junction channel
    • Protein or peptide: Gap junction beta-1 protein,Gap junction beta-1 protein,Green fluorescent protein

-
Supramolecule #1: A dodecameric complex of connexin-32 (Cx32) W3S mutant gap juncti...

SupramoleculeName: A dodecameric complex of connexin-32 (Cx32) W3S mutant gap junction channel
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Gap junction beta-1 protein,Gap junction beta-1 protein,Green flu...

MacromoleculeName: Gap junction beta-1 protein,Gap junction beta-1 protein,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 63.228297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNSTGLYTLL SGVNRHSTAI GRVWLSVIFI FRIMVLVVAA ESVWGDEKSS FICNTLQPGC NSVCYDQFFP ISHVRLWSLQ LILVSTPAL LVAMHVAHQQ HIEKKMLRLE GHGDPLHLEE VKRHKVHISG TLWWTYVISV VFRLLFEAVF MYVFYLLYPG Y AMVRLVKC ...String:
MNSTGLYTLL 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / 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: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 68649
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more