5AW9

Kinetics by X-ray crystallography: native E2.MgF42-.2K+ crystal for Rb+ bound crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


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Literature

Sequential substitution of K(+) bound to Na(+),K(+)-ATPase visualized by X-ray crystallography.

Ogawa, H.Cornelius, F.Hirata, A.Toyoshima, C.

(2015) Nat Commun 6: 8004-8004

  • DOI: 10.1038/ncomms9004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Na(+),K(+)-ATPase transfers three Na(+) from the cytoplasm into the extracellular medium and two K(+) in the opposite direction per ATP hydrolysed. The binding and release of Na(+) and K(+) are all thought to occur sequentially. Here we demonstrate b ...

    Na(+),K(+)-ATPase transfers three Na(+) from the cytoplasm into the extracellular medium and two K(+) in the opposite direction per ATP hydrolysed. The binding and release of Na(+) and K(+) are all thought to occur sequentially. Here we demonstrate by X-ray crystallography of the ATPase in E2·MgF4(2-)·2K(+), a state analogous to E2·Pi·2K(+), combined with isotopic measurements, that the substitution of the two K(+) with congeners in the extracellular medium indeed occurs at different rates, substantially faster at site II. An analysis of thermal movements of protein atoms in the crystal shows that the M3-M4E helix pair opens and closes the ion pathway leading to the extracellular medium, allowing K(+) at site II to be substituted first. Taken together, these results indicate that site I K(+) is the first cation to bind to the empty cation-binding sites after releasing three Na(+).


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Na, K-ATPase alpha subunit
A
1028Squalus acanthiasMutation(s): 0 
Gene Names: atn1
EC: 3.6.3.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; shark
Find proteins for Q4H132 (Squalus acanthias)
Go to UniProtKB:  Q4H132
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Na+,K+-ATPase beta subunit
B
305Squalus acanthiasMutation(s): 0 
Gene Names: atp1b1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; shark
Find proteins for C4IX13 (Squalus acanthias)
Go to UniProtKB:  C4IX13
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Phospholemman-like protein
G
74Squalus acanthiasMutation(s): 0 
Gene Names: fxyd10
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; shark
Find proteins for Q70Q12 (Squalus acanthias)
Go to UniProtKB:  Q70Q12
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MF4
Query on MF4

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Download CCD File 
A
TETRAFLUOROMAGNESATE(2-)
MAGNESIUMTETRAFLUORIDE
F4 Mg
XVYWAXYEHHUKQW-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CLR
Query on CLR

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Download CCD File 
B
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 219.972α = 90.00
b = 50.666β = 104.50
c = 163.066γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology of JapanJapan--
The Danish Medical Research FoundationDenmark--
The Danish Agency for Science Technology and InnovationDenmark--
The Novo Nordisk FoundationDenmark--

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release