4HYT

Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the high-affinity Na+,K+-ATPase-ouabain complex with Mg2+ bound in the cation binding site.

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

(2013) Proc Natl Acad Sci U S A 110: 10958-10963

  • DOI: 10.1073/pnas.1222308110
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Na(+),K(+)-ATPase maintains electrochemical gradients for Na(+) and K(+) that are critical for animal cells. Cardiotonic steroids (CTSs), widely used in the clinic and recently assigned a role as endogenous regulators of intracellular processes, ...

    The Na(+),K(+)-ATPase maintains electrochemical gradients for Na(+) and K(+) that are critical for animal cells. Cardiotonic steroids (CTSs), widely used in the clinic and recently assigned a role as endogenous regulators of intracellular processes, are highly specific inhibitors of the Na(+),K(+)-ATPase. Here we describe a crystal structure of the phosphorylated pig kidney Na(+),K(+)-ATPase in complex with the CTS representative ouabain, extending to 3.4 Å resolution. The structure provides key details on CTS binding, revealing an extensive hydrogen bonding network formed by the β-surface of the steroid core of ouabain and the side chains of αM1, αM2, and αM6. Furthermore, the structure reveals that cation transport site II is occupied by Mg(2+), and crystallographic studies indicate that Rb(+) and Mn(2+), but not Na(+), bind to this site. Comparison with the low-affinity [K2]E2-MgF(x)-ouabain structure [Ogawa et al. (2009) Proc Natl Acad Sci USA 106(33):13742-13747) shows that the CTS binding pocket of [Mg]E2P allows deep ouabain binding with possible long-range interactions between its polarized five-membered lactone ring and the Mg(2+). K(+) binding at the same site unwinds a turn of αM4, dragging residues Ile318-Val325 toward the cation site and thereby hindering deep ouabain binding. Thus, the structural data establish a basis for the interpretation of the biochemical evidence pointing at direct K(+)-Mg(2+) competition and explain the well-known antagonistic effect of K(+) on CTS binding.


    Organizational Affiliation

    Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, DK-8000 Aarhus C, Denmark.



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: 3.6.3.9 (PDB Primary Data), 7.2.2.13 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase-ouabain complex with Mg2+ in cation binding site
Find proteins for P05024 (Sus scrofa)
Go to UniProtKB:  P05024

Find similar proteins by: Sequence  |  Structure

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-ouabain complex with Mg2+ in cation binding site
Find proteins for P05027 (Sus scrofa)
Go to UniProtKB:  P05027

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Na+/K+ ATPase gamma subunit transcript variant a
E, G
65Sus scrofaMutation(s): 0 
Gene Names: FXYD2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase-ouabain complex with Mg2+ in cation binding site
Find proteins for Q58K79 (Sus scrofa)
Go to UniProtKB:  Q58K79
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
17F
Query on 17F

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

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A, C
OUABAIN
C29 H44 O12
LPMXVESGRSUGHW-HBYQJFLCSA-N
 Ligand Interaction
CE1
Query on CE1

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A, E
O-DODECANYL OCTAETHYLENE GLYCOL
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N
 Ligand Interaction
1AT
Query on 1AT

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A
beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside
C22 H40 O12
STVGXWVWPOLILC-LUQRLMJOSA-N
 Ligand Interaction
1DS
Query on 1DS

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A
1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside
C22 H40 O12
DSDLUVQAJPJFTK-AJFJJNJGSA-N
 Ligand Interaction
CLR
Query on CLR

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A, C, E, G
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-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
MG
Query on MG

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A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-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:  97   nM  BindingDB
OBNKi:  90   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.47α = 90
b = 118.08β = 90
c = 494.66γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
RemDAqdata collection
XDSdata reduction
diffractiondata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description