2ZXE | pdb_00002zxe

Crystal structure of the sodium - potassium pump in the E2.2K+.Pi state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.271 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Crystal structure of the sodium - potassium pump at 2.4 A resolution

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

(2009) Nature 459: 446-450

  • DOI: https://doi.org/10.1038/nature07939
  • Primary Citation Related Structures: 
    2ZXE

  • PubMed Abstract: 

    Sodium-potassium ATPase is an ATP-powered ion pump that establishes concentration gradients for Na(+) and K(+) ions across the plasma membrane in all animal cells by pumping Na(+) from the cytoplasm and K(+) from the extracellular medium. Such gradients are used in many essential processes, notably for generating action potentials. Na(+), K(+)-ATPase is a member of the P-type ATPases, which include sarcoplasmic reticulum Ca(2+)-ATPase and gastric H(+), K(+)-ATPase, among others, and is the target of cardiac glycosides. Here we describe a crystal structure of this important ion pump, from shark rectal glands, consisting of alpha- and beta-subunits and a regulatory FXYD protein, all of which are highly homologous to human ones. The ATPase was fixed in a state analogous to E2.2K(+).P(i), in which the ATPase has a high affinity for K(+) and still binds P(i), as in the first crystal structure of pig kidney enzyme at 3.5 A resolution. Clearly visualized now at 2.4 A resolution are coordination of K(+) and associated water molecules in the transmembrane binding sites and a phosphate analogue (MgF(4)(2-)) in the phosphorylation site. The crystal structure shows that the beta-subunit has a critical role in K(+) binding (although its involvement has previously been suggested) and explains, at least partially, why the homologous Ca(2+)-ATPase counter-transports H(+) rather than K(+), despite the coordinating residues being almost identical.


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

Macromolecule Content 

  • Total Structure Weight: 157.99 kDa 
  • Atom Count: 10,340 
  • Modeled Residue Count: 1,296 
  • Deposited Residue Count: 1,407 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Na, K-ATPase alpha subunit1,028Squalus acanthiasMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q4H132 (Squalus acanthias)
Explore Q4H132 
Go to UniProtKB:  Q4H132
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4H132
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Na+,K+-ATPase beta subunit305Squalus acanthiasMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C4IX13 (Squalus acanthias)
Explore C4IX13 
Go to UniProtKB:  C4IX13
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4IX13
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Phospholemman-like proteinC [auth G]74Squalus acanthiasMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q70Q12 (Squalus acanthias)
Explore Q70Q12 
Go to UniProtKB:  Q70Q12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70Q12
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G07375KG
GlyCosmos: G07375KG
GlyGen: G07375KG

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR

Query on CLR



Download:Ideal Coordinates CCD File
J [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
K [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MF4

Query on MF4



Download:Ideal Coordinates CCD File
E [auth A]TETRAFLUOROMAGNESATE(2-)
F4 Mg
XVYWAXYEHHUKQW-UHFFFAOYSA-J
K

Query on K



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.271 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.815α = 90
b = 50.914β = 105.12
c = 163.786γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary