Biological Assembly 1  

Global Symmetry: Dihedral - D6  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 504 kDa 
• Atom Count: 16,284 
• Modelled Residue Count: 1,992 
• Deposited Residue Count: 4,116 
• Unique protein chains: 1

 7XKI

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

• PDB DOI:  https://doi.org/10.2210/pdb7XKI/pdb
• EM Map EMD-33254: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• Deposited: 2022-04-19 Released: 2023-03-22 
• Deposition Author(s): Cho, H.J., Lee, S.N., Jeong, H., Ryu, B., Lee, H.J., Woo, J.S., Lee, H.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

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

Literature

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

• PubMed: 36906653 
• DOI: https://doi.org/10.1038/s41467-023-37040-8
• Primary Citation of Related Structures:  
  7XKI, 7XKK, 7XKT, 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.

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Organizational Affiliation: 

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gap junction delta-2 protein,Soluble cytochrome b562	A, B, C, D, E, F, G, H, I, J, K, L	343	Homo sapiens, Escherichia coli	Mutation(s): 3  Gene Names: GJD2, GJA9, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL4 (Homo sapiens) Explore Q9UKL4  Go to UniProtKB:  Q9UKL4
PHAROS:  Q9UKL4
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
UniProt Groups	P0ABE7Q9UKL4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MC3 (Subject of Investigation/LOI)	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]	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE C36 H72 N O8 P CITHEXJVPOWHKC-UUWRZZSWSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Cho, H.J., Lee, S.N., Jeong, H., Ryu, B., Lee, H.J., Woo, J.S., Lee, H.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2022R1A2B5B02002529
National Research Foundation (NRF, Korea)	Korea, Republic Of	2018R1C1B6004447

Revision History  

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