2PTM | pdb_00002ptm

Structure and rearrangements in the carboxy-terminal region of SpIH channels


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.242 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.183 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure and rearrangements in the carboxy-terminal region of SpIH channels.

Flynn, G.E.Black, K.D.Islas, L.D.Sankaran, B.Zagotta, W.N.

(2007) Structure 15: 671-682

  • DOI: https://doi.org/10.1016/j.str.2007.04.008
  • Primary Citation Related Structures: 
    2PTM, 2Q0A

  • PubMed Abstract: 

    Hyperpolarization-activated cyclic nucleotide-modulated (HCN) ion channels regulate the spontaneous firing activity and electrical excitability of many cardiac and neuronal cells. The modulation of HCN channel opening by the direct binding of cAMP underlies many physiological processes such as the autonomic regulation of the heart rate. Here we use a combination of X-ray crystallography and electrophysiology to study the allosteric mechanism for cAMP modulation of HCN channels. SpIH is an invertebrate HCN channel that is activated fully by cAMP, but only partially by cGMP. We exploited the partial agonist action of cGMP on SpIH to reveal the molecular mechanism for cGMP specificity of many cyclic nucleotide-regulated enzymes. Our results also elaborate a mechanism for the allosteric conformational change in the cyclic nucleotide-binding domain and a mechanism for partial agonist action. These mechanisms will likely extend to other cyclic nucleotide-regulated channels and enzymes as well.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 23.78 kDa 
  • Atom Count: 1,777 
  • Modeled Residue Count: 192 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hyperpolarization-activated (Ih) channel198Strongylocentrotus purpuratusMutation(s): 0 
UniProt
Find proteins for O76977 (Strongylocentrotus purpuratus)
Explore O76977 
Go to UniProtKB:  O76977
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76977
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CMP

Query on CMP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
NCO

Query on NCO



Download:Ideal Coordinates CCD File
B [auth A]COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.242 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.183 (DCC) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.354α = 90
b = 92.354β = 90
c = 63.646γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-07-28
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description