4KL1

HCN4 CNBD in complex with cGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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]
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
Q [auth D],
R [auth D]
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 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • 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 


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