4RET

Crystal structure of the Na,K-ATPase E2P-digoxin complex with bound magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures and characterization of digoxin- and bufalin-bound Na+,K+-ATPase compared with the ouabain-bound complex.

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

(2015) Proc.Natl.Acad.Sci.USA 112: 1755-1760

  • DOI: 10.1073/pnas.1422997112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cardiotonic steroids (CTSs) are specific and potent inhibitors of the Na(+),K(+)-ATPase, with highest affinity to the phosphoenzyme (E2P) forms. CTSs are comprised of a steroid core, which can be glycosylated, and a varying number of substituents, in ...

    Cardiotonic steroids (CTSs) are specific and potent inhibitors of the Na(+),K(+)-ATPase, with highest affinity to the phosphoenzyme (E2P) forms. CTSs are comprised of a steroid core, which can be glycosylated, and a varying number of substituents, including a five- or six-membered lactone. These functionalities have specific influence on the binding properties. We report crystal structures of the Na(+),K(+)-ATPase in the E2P form in complex with bufalin (a nonglycosylated CTS with a six-membered lactone) and digoxin (a trisaccharide-conjugated CTS with a five-membered lactone) and compare their characteristics and binding kinetics with the previously described E2P-ouabain complex to derive specific details and the general mechanism of CTS binding and inhibition. CTSs block the extracellular cation exchange pathway, and cation-binding sites I and II are differently occupied: A single Mg(2+) is bound in site II of the digoxin and ouabain complexes, whereas both sites are occupied by K(+) in the E2P-bufalin complex. In all complexes, αM4 adopts a wound form, characteristic for the E2P state and favorable for high-affinity CTS binding. We conclude that the occupants of the cation-binding site and the type of the lactone substituent determine the arrangement of αM4 and hypothesize that winding/unwinding of αM4 represents a trigger for high-affinity CTS binding. We find that the level of glycosylation affects the depth of CTS binding and that the steroid core substituents fine tune the configuration of transmembrane helices αM1-2.


    Organizational Affiliation

    Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, DK-8000 Aarhus C, Denmark; Departments of Biomedicine and.,Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, DK-8000 Aarhus C, Denmark; Departments of Biomedicine and pn@mbg.au.dk nf@biomed.au.dk.,Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, DK-8000 Aarhus C, Denmark; Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark; and.,Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, DK-8000 Aarhus C, Denmark; Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark; and Danish Research Institute for Translational Neuroscience, Nordic-European Molecular Biology Laboratory Partnership of Molecular Medicine, DK-8000 Aarhus C, Denmark pn@mbg.au.dk nf@biomed.au.dk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit alpha-1
A, C
1021Sus 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
303Sus 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
65Sus 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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

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Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
17F
Query on 17F

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Download CCD File 
A, B
O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine
1,2-Dioleoyl-sn-glycero-3-phospho-L-serine
C42 H78 N O10 P
WTBFLCSPLLEDEM-JIDRGYQWSA-N
 Ligand Interaction
DGX
Query on DGX

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A, C
DIGOXIN
C41 H64 O14
LTMHDMANZUZIPE-PUGKRICDSA-N
 Ligand Interaction
MG
Query on MG

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A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CLR
Query on CLR

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Download CCD File 
A, C, G
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-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 %)
DGXIC50: 500 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.240α = 90.00
b = 118.350β = 90.00
c = 494.090γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
Diffractiondata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references
  • Version 1.2: 2015-02-25
    Type: Database references