4HBN

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 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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: 10.1016/j.str.2012.09.017
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4A205Homo sapiensMutation(s): 1 
Gene Names: HCN4
Find proteins for Q9Y3Q4 (Homo sapiens)
Explore Q9Y3Q4 
Go to UniProtKB:  Q9Y3Q4
NIH Common Fund Data Resources
PHAROS:  Q9Y3Q4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMP
Query on CMP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CMPKd :  800   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • 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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release