6SYG

Crystal structure of the Cyclic Nucleotide-Binding Homology Domain of the human KCNH2 channel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Structure of KCNH2 cyclic nucleotide-binding homology domain reveals a functionally vital salt-bridge.

Ben-Bassat, A.Giladi, M.Haitin, Y.

(2020) J Gen Physiol 152

  • DOI: https://doi.org/10.1085/jgp.201912505
  • Primary Citation of Related Structures:  
    6SYG

  • PubMed Abstract: 

    Human KCNH2 channels (hKCNH2, ether-à-go-go [EAG]-related gene, hERG) are best known for their contribution to cardiac action potential repolarization and have key roles in various pathologies. Like other KCNH family members, hKCNH2 channels contain a unique intracellular complex, consisting of an N-terminal eag domain and a C-terminal cyclic nucleotide-binding homology domain (CNBHD), which is crucial for channel function. Previous studies demonstrated that the CNBHD is occupied by an intrinsic ligand motif, in a self-liganded conformation, providing a structural mechanism for the lack of KCNH channel regulation by cyclic nucleotides. While there have been significant advancements in the structural and functional characterization of the CNBHD of KCNH channels, a high-resolution structure of the hKCNH2 intracellular complex has been missing. Here, we report the 1.5 Å resolution structure of the hKCNH2 channel CNBHD. The structure reveals the canonical fold shared by other KCNH family members, where the spatial organization of the intrinsic ligand is preserved within the β-roll region. Moreover, measurements of small-angle x-ray scattering profile in solution, as well as comparison with a recent NMR analysis of hKCNH2, revealed high agreement with the crystallographic structure, indicating an overall low flexibility in solution. Importantly, we identified a novel salt-bridge (E807-R863) which was not previously resolved in the NMR and cryo-EM structures. Electrophysiological analysis of charge-reversal mutations revealed the bridge's crucial role in hKCNH2 function. Moreover, comparison with other KCNH members revealed the structural conservation of this salt-bridge, consistent with its functional significance. Together with the available structure of the mouse KCNH1 intracellular complex and previous electrophysiological and spectroscopic studies of KCNH family members, we propose that this salt-bridge serves as a strategically positioned linchpin to support both the spatial organization of the intrinsic ligand and the maintenance of the intracellular complex interface.


  • Organizational Affiliation

    Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel subfamily H member 2135Homo sapiensMutation(s): 0 
Gene Names: KCNH2ERGERG1HERG
UniProt
Find proteins for O08962 (Rattus norvegicus)
Explore O08962 
Go to UniProtKB:  O08962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08962
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.493α = 90
b = 90.649β = 90
c = 61.111γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1721/16
Israel Science FoundationIsrael1775/12
Other privateIsraelICRF 01214
German-Israeli Foundation for Research and DevelopmentIsraelI-2425-418.13/2016

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 2.0: 2020-03-18
    Changes: Atomic model, Data collection, Database references, Source and taxonomy, Structure summary
  • Version 2.1: 2020-04-15
    Changes: Database references
  • Version 3.0: 2020-04-29
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 3.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description