4XE5

Crystal structure of the Na,K-ATPase from bovine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.901 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.322 

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.,Sect.F 72: 282-287

  • DOI: 10.1107/S2053230X1600279X

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit alpha-1
A
1021Bos taurusGene Names: ATP1A1
EC: 3.6.3.9
Find proteins for Q08DA1 (Bos taurus)
Go to Gene View: ATP1A1
Go to UniProtKB:  Q08DA1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit beta
B
303Bos taurusGene Names: ATP1B1
Find proteins for G3MWR4 (Bos taurus)
Go to Gene View: ATP1B1
Go to UniProtKB:  G3MWR4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Sodium/potassium-transporting ATPase subunit gamma
G
58Bos taurusGene Names: FXYD2 (ATP1C, ATP1G1)
Find proteins for Q04645 (Bos taurus)
Go to Gene View: FXYD2
Go to UniProtKB:  Q04645
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
OBN
Query on OBN

Download SDF File 
Download CCD File 
A
OUABAIN
C29 H44 O12
LPMXVESGRSUGHW-HBYQJFLCSA-N
 Ligand Interaction
CLR
Query on CLR

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Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BFD
Query on BFD
A
L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.901 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.322 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 64.750α = 90.00
b = 301.070β = 90.00
c = 242.290γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
PHASERphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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