9QNT | pdb_00009qnt

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Lipid dependence of connexin-32 gap junction channel conformations.

Lavriha, P.Fluri, C.Hernandez Gonzalez, J.E.Korkhov, V.M.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-67004-z
  • Primary Citation of Related Structures:  
    9QN9, 9QND, 9QNF, 9QNT

  • PubMed 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 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.


  • Organizational Affiliation
    • Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gap junction beta-1 protein,Green fluorescent protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
566Homo sapiensAequorea victoria
This entity is chimeric
Mutation(s): 0 
Gene Names: GJB1CX32GFP
UniProt & NIH Common Fund Data Resources
Find proteins for P08034 (Homo sapiens)
Explore P08034 
Go to UniProtKB:  P08034
PHAROS:  P08034
GTEx:  ENSG00000169562 
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212P08034
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
AA [auth H]
DA [auth I]
FA [auth J]
HA [auth K]
IA [auth L]
AA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
IA [auth L],
M [auth A],
O [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
BA [auth H]
CA [auth I]
EA [auth J]
GA [auth K]
JA [auth L]
BA [auth H],
CA [auth I],
EA [auth J],
GA [auth K],
JA [auth L],
N [auth A],
P [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland184951

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release