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: 4.60 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.273 

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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: https://doi.org/10.1016/j.jsb.2010.12.004
  • Primary Citation of Related Structures:  
    3N23

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-1A,
D [auth C]
992Sus scrofaMutation(s): 0 
EC: 3.6.3.9 (PDB Primary Data), 7.2.2.13 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P05024 (Sus scrofa)
Explore P05024 
Go to UniProtKB:  P05024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05024
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1B,
E [auth D]
277Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05027 (Sus scrofa)
Explore P05027 
Go to UniProtKB:  P05027
Entity Groups  
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UniProt GroupP05027
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Na+/K+ ATPase gamma subunit transcript variant aC [auth G],
F [auth E]
31Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q58K79 (Sus scrofa)
Explore Q58K79 
Go to UniProtKB:  Q58K79
Entity Groups  
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UniProt GroupQ58K79
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PHD
Query on PHD
A,
D [auth C]
L-PEPTIDE LINKINGC4 H8 N O7 PASP
Binding Affinity Annotations 
IDSourceBinding Affinity
OBN BindingDB:  3N23 Ki: min: 90, max: 97 (nM) from 2 assay(s)
IC50: min: 4.3, max: 4300 (nM) from 4 assay(s)
PDBBind:  3N23 Kd: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.16α = 90
b = 118.93β = 90
c = 494.1γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
CNSrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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