4KL1

HCN4 CNBD in complex with cGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.272 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PCGClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Cyclic dinucleotides bind the C-linker of HCN4 to control channel cAMP responsiveness.

Lolicato, M.Bucchi, A.Arrigoni, C.Zucca, S.Nardini, M.Schroeder, I.Simmons, K.Aquila, M.DiFrancesco, D.Bolognesi, M.Schwede, F.Kashin, D.Fishwick, C.W.Johnson, A.P.Thiel, G.Moroni, A.

(2014) Nat Chem Biol 10: 457-462

  • DOI: https://doi.org/10.1038/nchembio.1521
  • Primary Citation of Related Structures:  
    4KL1

  • PubMed Abstract: 

    cAMP mediates autonomic regulation of heart rate by means of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which underlie the pacemaker current If. cAMP binding to the C-terminal cyclic nucleotide binding domain enhances HCN open probability through a conformational change that reaches the pore via the C-linker. Using structural and functional analysis, we identified a binding pocket in the C-linker of HCN4. Cyclic dinucleotides, an emerging class of second messengers in mammals, bind the C-linker pocket (CLP) and antagonize cAMP regulation of the channel. Accordingly, cyclic dinucleotides prevent cAMP regulation of If in sinoatrial node myocytes, reducing heart rate by 30%. Occupancy of the CLP hence constitutes an efficient mechanism to hinder β-adrenergic stimulation on If. Our results highlight the regulative role of the C-linker and identify a potential drug target in HCN4. Furthermore, these data extend the signaling scope of cyclic dinucleotides in mammals beyond their first reported role in innate immune system.


  • Organizational Affiliation

    1] Department of Biosciences, University of Milan, Milan, Italy. [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
A, B, C, D
199Homo sapiensMutation(s): 0 
Gene Names: HCN4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3Q4 (Homo sapiens)
Explore Q9Y3Q4 
Go to UniProtKB:  Q9Y3Q4
PHAROS:  Q9Y3Q4
GTEx:  ENSG00000138622 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3Q4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCG
Query on PCG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
K [auth B]
L [auth C]
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth C],
O [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
P [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.1α = 90
b = 99.03β = 90
c = 109.57γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PCGClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection
  • Version 1.4: 2024-11-06
    Changes: Structure summary