8ZYQ

Cryo-EM Structure of pimozide-bound hERG Channel

• PDB DOI: https://doi.org/10.2210/pdb8ZYQ/pdb
• EM Map EMD-60576: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-06-18 Released: 2024-09-18 
• Deposition Author(s): Miyashita, Y., Moriya, T., Kato, T., Kawasaki, M., Yasuda, Y., Adachi, N., Suzuki, K., Ogasawara, S., Saito, T., Senda, T., Murata, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Improved higher resolution Cryo-EM structures reveal the binding modes of hERG Channel Inhibitors

Miyashita, Y., Moriya, T., Kato, T., Kawasaki, M., Yasuda, Y., Adachi, N., Suzuki, K., Ogasawara, S., Saito, T., Senda, T., Murata, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 367.63 kDa 
• Atom Count: 6,329 
• Modelled Residue Count: 796 
• Deposited Residue Count: 3,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium voltage-gated channel subfamily H member 2	A, B, C, D	820	Homo sapiens	Mutation(s): 0  Gene Names: KCNH2, ERG, ERG1, HERG Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q12809 (Homo sapiens) Explore Q12809  Go to UniProtKB:  Q12809
PHAROS:  Q12809 GTEx:  ENSG00000055118

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1II (Subject of Investigation/LOI)	E [auth B]	3-[1-[4,4-bis(4-fluorophenyl)butyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one C28 H29 F2 N3 O YVUQSNJEYSNKRX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Miyashita, Y., Moriya, T., Kato, T., Kawasaki, M., Yasuda, Y., Adachi, N., Suzuki, K., Ogasawara, S., Saito, T., Senda, T., Murata, T.

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

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release