4XE5

Crystal structure of the Na,K-ATPase from bovine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.322 
  • R-Value Observed: 0.323 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

Gregersen, J.L.Mattle, D.Fedosova, N.U.Nissen, P.Reinhard, L.

(2016) Acta Crystallogr F Struct Biol Commun 72: 282-287

  • DOI: 10.1107/S2053230X1600279X
  • Primary Citation of Related Structures:  
    4XE5

  • PubMed Abstract: 
  • Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+) ...

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions.


    Organizational Affiliation

    Centre for Membrane Pumps in Cells and Disease - PUMPkin, Danish National Research Foundation, Denmark.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-1A1021Bos taurusMutation(s): 0 
Gene Names: ATP1A1
EC: 3.6.3.9 (PDB Primary Data), 7.2.2.13 (UniProt)
Find proteins for Q08DA1 (Bos taurus)
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Go to UniProtKB:  Q08DA1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit betaB303Bos taurusMutation(s): 0 
Gene Names: ATP1B1
Find proteins for G3MWR4 (Bos taurus)
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Go to UniProtKB:  G3MWR4
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit gammaG58Bos taurusMutation(s): 0 
Gene Names: FXYD2ATP1CATP1G1
Find proteins for Q04645 (Bos taurus)
Explore Q04645 
Go to UniProtKB:  Q04645
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 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

Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BFD
Query on BFD
AL-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
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: 3.90 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.322 
  • R-Value Observed: 0.323 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.75α = 90
b = 301.07β = 90
c = 242.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2016-04-13
    Changes: Database references
  • Version 1.3: 2016-07-20
    Changes: Database references
  • Version 1.4: 2018-01-17
    Changes: Data collection