3A3Y

Crystal structure of the sodium-potassium pump with bound potassium and ouabain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the sodium-potassium pump (Na+,K+-ATPase) with bound potassium and ouabain.

Ogawa, H.Shinoda, T.Cornelius, F.Toyoshima, C.

(2009) Proc Natl Acad Sci U S A 106: 13742-13747

  • DOI: 10.1073/pnas.0907054106
  • Primary Citation of Related Structures:  
    3A3Y

  • PubMed Abstract: 
  • The sodium-potassium pump (Na(+),K(+)-ATPase) is responsible for establishing Na(+) and K(+) concentration gradients across the plasma membrane and therefore plays an essential role in, for instance, generating action potentials. Cardiac glycosides, ...

    The sodium-potassium pump (Na(+),K(+)-ATPase) is responsible for establishing Na(+) and K(+) concentration gradients across the plasma membrane and therefore plays an essential role in, for instance, generating action potentials. Cardiac glycosides, prescribed for congestive heart failure for more than 2 centuries, are efficient inhibitors of this ATPase. Here we describe a crystal structure of Na(+),K(+)-ATPase with bound ouabain, a representative cardiac glycoside, at 2.8 A resolution in a state analogous to E2.2K(+).Pi. Ouabain is deeply inserted into the transmembrane domain with the lactone ring very close to the bound K(+), in marked contrast to previous models. Due to antagonism between ouabain and K(+), the structure represents a low-affinity ouabain-bound state. Yet, most of the mutagenesis data obtained with the high-affinity state are readily explained by the present crystal structure, indicating that the binding site for ouabain is essentially the same. According to a homology model for the high affinity state, it is a closure of the binding cavity that confers a high affinity.


    Organizational Affiliation

    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Na, K-ATPase alpha subunitA1028Squalus acanthiasMutation(s): 0 
Gene Names: atn1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase with bound ouabain and K+
Find proteins for Q4H132 (Squalus acanthias)
Explore Q4H132 
Go to UniProtKB:  Q4H132
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NA+,K+-ATPASE BETA SUBUNITB305Squalus acanthiasMutation(s): 0 
Gene Names: atp1b1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase with bound ouabain and K+
Find proteins for C4IX13 (Squalus acanthias)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholemman-like proteinG74Squalus acanthiasMutation(s): 0 
Gene Names: fxyd10
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase with bound ouabain and K+
Find proteins for Q70Q12 (Squalus acanthias)
Explore Q70Q12 
Go to UniProtKB:  Q70Q12
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OBN
Query on OBN

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A
OUABAIN
C29 H44 O12
LPMXVESGRSUGHW-HBYQJFLCSA-N
 Ligand Interaction
CLR
Query on CLR

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B
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
NAG
Query on NAG

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B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MF4
Query on MF4

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A
TETRAFLUOROMAGNESATE(2-)
F4 Mg
XVYWAXYEHHUKQW-UHFFFAOYSA-J
 Ligand Interaction
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OBNKi:  90   nM  BindingDB
OBNKi:  97   nM  BindingDB
OBNKd :  0.699999988079071   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.884α = 90
b = 50.72β = 104.63
c = 163.342γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary