8INZ

Cryo-EM structure of human HCN3 channel in apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of human HCN3 channel and its regulation by cAMP.

Yu, B.Lu, Q.Li, J.Cheng, X.Hu, H.Li, Y.Che, T.Hua, Y.Jiang, H.Zhang, Y.Xian, C.Yang, T.Fu, Y.Chen, Y.Nan, W.McCormick, P.J.Xiong, B.Duan, J.Zeng, B.Li, Y.Fu, Y.Zhang, J.

(2024) J Biol Chem 300: 107288-107288

  • DOI: https://doi.org/10.1016/j.jbc.2024.107288
  • Primary Citation of Related Structures:  
    8INZ

  • PubMed Abstract: 

    HCN channels are important for regulating heart rhythm and nerve activity and have been studied as potential drug targets for treating depression, arrhythmia, nerve pain, and epilepsy. Despite possessing unique pharmacological properties, HCN channels share common characteristics in that they are activated by hyperpolarization and modulated by cAMP and other membrane lipids. However, the mechanisms of how these ligands bind and modulate HCN channels are unclear. In this study, we solved structures of full-length human HCN3 using cryo-EM and captured two different states, including a state without any ligand bound and a state with cAMP bound. Our structures reveal the novel binding sites for cholesteryl hemisuccinate in apo state and show how cholesteryl hemisuccinate and cAMP binding cause conformational changes in different states. These findings explain how these small modulators are sensed in mammals at the molecular level. The results of our study could help to design more potent and specific compounds to influence HCN channel activity and offer new therapeutic possibilities for diseases that lack effective treatment.


  • Organizational Affiliation

    The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China; The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3A [auth C],
B [auth A],
C [auth B],
D
774Homo sapiensMutation(s): 0 
Gene Names: HCN3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P1Z3 (Homo sapiens)
Explore Q9P1Z3 
Go to UniProtKB:  Q9P1Z3
PHAROS:  Q9P1Z3
GTEx:  ENSG00000143630 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P1Z3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VX9 (Subject of Investigation/LOI)
Query on VX9

Download Ideal Coordinates CCD File 
E [auth C],
F [auth A],
G [auth B],
H [auth D]
4-[[(2~{S},4~{a}~{R},6~{S},8~{a}~{S})-6-[(4~{S},5~{R})-4-[(2~{S})-butan-2-yl]-5,9-dimethyl-decyl]-4~{a}-methyl-2,3,4,5,6,7,8,8~{a}-octahydro-1~{H}-naphthalen-2-yl]oxy]-4-oxidanylidene-butanoic acid
C31 H56 O4
CAWMEKGHGQMGSF-ZGQNKYPXSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references