3N23

Crystal structure of the high affinity complex between ouabain and the E2P form of the sodium-potassium pump


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.6 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the high affinity binding of cardiotonic steroids to the Na+,K+-ATPase.

Yatime, L.Laursen, M.Morth, J.P.Esmann, M.Nissen, P.Fedosova, N.U.

(2011) J.Struct.Biol. 174: 296-306

  • DOI: 10.1016/j.jsb.2010.12.004

  • PubMed Abstract: 
  • The Na+,K+-ATPase belongs to the P-ATPase family, whose characteristic property is the formation of a phosphorylated intermediate. The enzyme is also a defined target for cardiotonic steroids which inhibit its functional activity and initiate intrace ...

    The Na+,K+-ATPase belongs to the P-ATPase family, whose characteristic property is the formation of a phosphorylated intermediate. The enzyme is also a defined target for cardiotonic steroids which inhibit its functional activity and initiate intracellular signaling. Here we describe the 4.6 Å resolution crystal structure of the pig kidney Na+,K+-ATPase in its phosphorylated form stabilized by high affinity binding of the cardiotonic steroid ouabain. The steroid binds to a site formed at transmembrane segments αM1-αM6, plugging the ion pathway from the extracellular side. This structure differs from the previously reported low affinity complex with potassium. Most importantly, the A domain has rotated in response to phosphorylation and αM1-2 move towards the ouabain molecule, providing for high affinity interactions and closing the ion pathway from the extracellular side. The observed re-arrangements of the Na+,K+-ATPase stabilized by cardiotonic steroids may affect protein-protein interactions within the intracellular signal transduction networks.


    Organizational Affiliation

    Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit alpha-1
A, C
992Sus scrofaMutation(s): 0 
Gene Names: ATP1A1
EC: 7.2.2.13
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for P05024 (Sus scrofa)
Go to Gene View: ATP1A1
Go to UniProtKB:  P05024
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit beta-1
B, D
277Sus scrofaMutation(s): 0 
Gene Names: ATP1B1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for P05027 (Sus scrofa)
Go to Gene View: ATP1B1
Go to UniProtKB:  P05027
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Na+/K+ ATPase gamma subunit transcript variant a
G, E
31Sus scrofaMutation(s): 0 
Gene Names: FXYD2
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for Q58K79 (Sus scrofa)
Go to Gene View: FXYD2
Go to UniProtKB:  Q58K79
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
OBN
Query on OBN

Download SDF File 
Download CCD File 
A, C
OUABAIN
C29 H44 O12
LPMXVESGRSUGHW-HBYQJFLCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHD
Query on PHD
A, C
L-PEPTIDE LINKINGC4 H8 N O7 PASP
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OBNKi: 90 - 97 nM (87) BINDINGDB
OBNKd: 3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.6 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.272 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 117.160α = 90.00
b = 118.930β = 90.00
c = 494.100γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
MxCuBEdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-09-17
    Type: Database references