4HBN | pdb_00004hbn

Crystal structure of the human HCN4 channel C-terminus carrying the S672R mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.297 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.257 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

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Literature

Local and Global Interpretations of a Disease-Causing Mutation near the Ligand Entry Path in Hyperpolarization-Activated cAMP-Gated Channel.

Xu, X.Marni, F.Wu, S.Su, Z.Musayev, F.Shrestha, S.Xie, C.Gao, W.Liu, Q.Zhou, L.

(2012) Structure 20: 2116-2123

  • DOI: https://doi.org/10.1016/j.str.2012.09.017
  • Primary Citation Related Structures: 
    4HBN

  • PubMed Abstract: 

    Hyperpolarization-activated, cAMP-gated (HCN) channels sense membrane potential and intracellular cAMP levels. A mutation identified in the cAMP binding domain (CNBD) of the human HCN4 channel, S672R, severely reduces the heart rate, but the molecular mechanism has been unclear. Our biochemical binding assays on isolated CNBD and patch-clamp recordings on the functional channel show that S672R reduces cAMP binding. The crystal structure of the mutant CNBD revealed no global changes except a disordered loop on the cAMP entry path. To address this localized structural perturbation at a whole protein level, we studied the activity-dependent dynamic interaction between cAMP and the functional channel using the patch-clamp fluorometry technique. S672R reduces the binding of cAMP to the channels in the resting state and significantly increases the unbinding rate during channel deactivation. This study on a disease-causing mutation illustrates the important roles played by the structural elements on the ligand entry-exit path in stabilizing the bound ligand in the binding pocket.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA.

Macromolecule Content 

  • Total Structure Weight: 24.64 kDa 
  • Atom Count: 1,692 
  • Modeled Residue Count: 199 
  • Deposited Residue Count: 205 
  • 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 4205Homo sapiensMutation(s): 1 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.297 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.257 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.467α = 90
b = 95.467β = 90
c = 115.99γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations