8XGD

Human Cx36/GJD2 gap junction channel with pore-lining N-terminal helices in porcine brain lipids.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 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

Mefloquine-induced conformational shift in Cx36 N-terminal helix leading to channel closure mediated by lipid bilayer.

Cho, H.J.Chung, D.K.Lee, H.H.

(2024) Nat Commun 15: 9223-9223

  • DOI: https://doi.org/10.1038/s41467-024-53587-6
  • Primary Citation of Related Structures:  
    8XGD, 8XGE, 8XGF, 8XGG, 8XGJ, 8XH8, 8XH9

  • PubMed Abstract: 

    Connexin 36 (Cx36) forms interneuronal gap junctions, establishing electrical synapses for rapid synaptic transmission. In disease conditions, inhibiting Cx36 gap junction channels (GJCs) is beneficial, as it prevents abnormal synchronous neuronal firing and apoptotic signal propagation, mitigating seizures and progressive cell death. Here, we present cryo-electron microscopy structures of human Cx36 GJC in complex with known channel inhibitors, such as mefloquine, arachidonic acid, and 1-hexanol. Notably, these inhibitors competitively bind to the binding pocket of the N-terminal helices (NTH), inducing a conformational shift from the pore-lining NTH (PLN) state to the flexible NTH (FN) state. This leads to the obstruction of the channel pore by flat double-layer densities of lipids. These studies elucidate the molecular mechanisms of how Cx36 GJC can be modulated by inhibitors, providing valuable insights into potential therapeutic applications.


  • Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gap junction delta-2 protein331Homo sapiensMutation(s): 0 
Gene Names: GJD2GJA9
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL4 (Homo sapiens)
Explore Q9UKL4 
Go to UniProtKB:  Q9UKL4
PHAROS:  Q9UKL4
GTEx:  ENSG00000159248 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKL4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MC3
Query on MC3

Download Ideal Coordinates CCD File 
AA [auth G]
AB [auth E]
AC [auth L]
BC [auth L]
CA [auth G]
AA [auth G],
AB [auth E],
AC [auth L],
BC [auth L],
CA [auth G],
CB [auth H],
CC [auth L],
DA [auth G],
DB [auth H],
DC [auth L],
EA [auth B],
EB [auth H],
EC [auth L],
FA [auth B],
GA [auth B],
GB [auth H],
HB [auth H],
IA [auth B],
IB [auth I],
JA [auth B],
JB [auth I],
KA [auth C],
KB [auth I],
LA [auth C],
M [auth A],
MA [auth C],
MB [auth I],
N [auth A],
NB [auth I],
O [auth A],
OA [auth C],
OB [auth J],
PA [auth C],
PB [auth J],
Q [auth A],
QA [auth D],
QB [auth J],
R [auth A],
RA [auth D],
S [auth F],
SA [auth D],
SB [auth J],
T [auth F],
TB [auth J],
U [auth F],
UA [auth D],
UB [auth K],
V [auth F],
VA [auth D],
VB [auth K],
W [auth F],
WA [auth E],
WB [auth K],
XA [auth E],
Y [auth G],
YA [auth E],
YB [auth K],
Z [auth G],
ZA [auth E],
ZB [auth K]
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
C36 H72 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
BA [auth G]
BB [auth E]
FB [auth H]
FC [auth L]
HA [auth B]
BA [auth G],
BB [auth E],
FB [auth H],
FC [auth L],
HA [auth B],
LB [auth I],
NA [auth C],
P [auth A],
RB [auth J],
TA [auth D],
X [auth F],
XB [auth K]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Samsung Science and Technology FoundationKorea, Republic OfSSTF-BA2101-13

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release