4KL1 | pdb_00004kl1

HCN4 CNBD in complex with cGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.272 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4KL1

Ligand Structure Quality Assessment 


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 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].

Macromolecule Content 

  • Total Structure Weight: 96.74 kDa 
  • Atom Count: 6,814 
  • Modeled Residue Count: 772 
  • Deposited Residue Count: 796 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.206 (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 


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