Human Cx36/GJD2 (N-terminal deletion BRIL-fused mutant) gap junction channel in soybean lipids (D6 symmetry)

Experimental Data Snapshot

  • Resolution: 3.40 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


Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel.

Lee, S.N.Cho, H.J.Jeong, H.Ryu, B.Lee, H.J.Kim, M.Yoo, J.Woo, J.S.Lee, H.H.

(2023) Nat Commun 14: 1347-1347

  • DOI: https://doi.org/10.1038/s41467-023-37040-8
  • Primary Citation of Related Structures:  
    7XKI, 7XKK, 7XKT, 7XL8, 7XNH, 7XNV, 8HKP

  • PubMed Abstract: 

    Connexin 36 (Cx36) is responsible for signal transmission in electrical synapses by forming interneuronal gap junctions. Despite the critical role of Cx36 in normal brain function, the molecular architecture of the Cx36 gap junction channel (GJC) is unknown. Here, we determine cryo-electron microscopy structures of Cx36 GJC at 2.2-3.6 Å resolutions, revealing a dynamic equilibrium between its closed and open states. In the closed state, channel pores are obstructed by lipids, while N-terminal helices (NTHs) are excluded from the pore. In the open state with pore-lining NTHs, the pore is more acidic than those in Cx26 and Cx46/50 GJCs, explaining its strong cation selectivity. The conformational change during channel opening also includes the α-to-π-helix transition of the first transmembrane helix, which weakens the protomer-protomer interaction. Our structural analyses provide high resolution information on the conformational flexibility of Cx36 GJC and suggest a potential role of lipids in the channel gating.

  • Organizational Affiliation

    Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gap junction delta-2 protein,Soluble cytochrome b562
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
343Homo sapiensEscherichia coliMutation(s): 3 
Gene Names: GJD2GJA9cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q9UKL4 (Homo sapiens)
Explore Q9UKL4 
Go to UniProtKB:  Q9UKL4
GTEx:  ENSG00000159248 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q9UKL4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MC3 (Subject of Investigation/LOI)
Query on MC3

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth K]
BA [auth D]
BB [auth K]
CA [auth E]
AA [auth D],
AB [auth K],
BA [auth D],
BB [auth K],
CA [auth E],
CB [auth K],
DA [auth E],
DB [auth K],
EA [auth E],
EB [auth L],
FA [auth E],
FB [auth L],
GA [auth F],
GB [auth L],
HA [auth F],
HB [auth L],
IA [auth F],
JA [auth F],
KA [auth G],
LA [auth G],
M [auth A],
MA [auth G],
N [auth A],
NA [auth G],
O [auth A],
OA [auth H],
P [auth A],
PA [auth H],
Q [auth B],
QA [auth H],
R [auth B],
RA [auth H],
S [auth B],
SA [auth I],
T [auth B],
TA [auth I],
U [auth C],
UA [auth I],
V [auth C],
VA [auth I],
W [auth C],
WA [auth J],
X [auth C],
XA [auth J],
Y [auth D],
YA [auth J],
Z [auth D],
ZA [auth J]
C36 H72 N O8 P
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2022R1A2B5B02002529
National Research Foundation (NRF, Korea)Korea, Republic Of2018R1C1B6004447

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release