7CN1

Cryo-EM structure of K+-bound hERG channel in the presence of astemizole

• PDB DOI:  https://doi.org/10.2210/pdb7CN1/pdb
• EM Map EMD-30413: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-07-29 Released: 2021-01-20 
• Deposition Author(s): Asai, T., Adachi, N., Moriya, T., Kawasaki, M., Suzuki, K., Senda, T., Murata, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structure of K + -Bound hERG Channel Complexed with the Blocker Astemizole.

Asai, T., Adachi, N., Moriya, T., Oki, H., Maru, T., Kawasaki, M., Suzuki, K., Chen, S., Ishii, R., Yonemori, K., Igaki, S., Yasuda, S., Ogasawara, S., Senda, T., Murata, T.

(2021) Structure 29: 203-212.e4

• PubMed: 33450182 
• DOI: https://doi.org/10.1016/j.str.2020.12.007
• Primary Citation of Related Structures:  
  7CN0, 7CN1


• PubMed Abstract: 
  

The hERG channel is a voltage-gated potassium channel involved in cardiac repolarization. Off-target hERG inhibition by drugs has become a critical issue in the pharmaceutical industry. The three-dimensional structure of the hERG channel was recently reported at 3.8-Å resolution using cryogenic electron microscopy (cryo-EM). However, the drug inhibition mechanism remains unclear because of the scarce structural information regarding the drug- and potassium-bound hERG channels. In this study, we obtained the cryo-EM density map of potassium-bound hERG channel complexed with astemizole, a well-known hERG inhibitor that increases risk of potentially fatal arrhythmia, at 3.5-Å resolution. The structure suggested that astemizole inhibits potassium conduction by binding directly below the selectivity filter. Furthermore, we propose a possible binding model of astemizole to the hERG channel and provide insights into the unusual sensitivity of hERG to several drugs.

---

Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan; Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 367.29 kDa 
• Atom Count: 6,290 
• Modelled Residue Count: 822 
• Deposited Residue Count: 3,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
potassium channel	A, B, C, D	820	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Asai, T., Adachi, N., Moriya, T., Kawasaki, M., Suzuki, K., Senda, T., Murata, T.

---

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101071
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101083
Japan Society for the Promotion of Science (JSPS)	Japan	18H05425

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-03-17
  Changes: Database references