6JXK

Rb+-bound E2-MgF state of the gastric proton pump (Wild-type)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A single K+-binding site in the crystal structure of the gastric proton pump.

Yamamoto, K.Dubey, V.Irie, K.Nakanishi, H.Khandelia, H.Fujiyoshi, Y.Abe, K.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.47701
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The gastric proton pump (H <sup>+ </sup>,K <sup>+ </sup>-ATPase), a P-type ATPase responsible for gastric acidification, mediates electro-neutral exchange of H <sup>+ </sup> and K <sup>+ </sup> coupled with ATP hydrolysis, but with an as yet undeterm ...

    The gastric proton pump (H + ,K + -ATPase), a P-type ATPase responsible for gastric acidification, mediates electro-neutral exchange of H + and K + coupled with ATP hydrolysis, but with an as yet undetermined transport stoichiometry. Here we show crystal structures at a resolution of 2.5 Å of the pump in the E2-P transition state, in which the counter-transporting cation is occluded. We found a single K + bound to the cation-binding site of the H + ,K + -ATPase, indicating an exchange of 1H + /1K + per hydrolysis of one ATP molecule. This fulfills the energy requirement for the generation of a six pH unit gradient across the membrane. The structural basis of K + recognition is resolved and supported by molecular dynamics simulations, establishing how the H + ,K + -ATPase overcomes the energetic challenge to generate an H + gradient of more than a million-fold-one of the highest cation gradients known in mammalian tissue-across the membrane.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan.,CeSPIA Inc, Tokyo, Japan.,Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Department of Physics, Chemistry and Pharmacy, PHYLIFE, University of Southern Denmark, Odense, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase alpha chain 1
A, E
987Sus scrofaMutation(s): 3 
Gene Names: ATP4A
EC: 7.2.2.19
Find proteins for P19156 (Sus scrofa)
Go to Gene View: ATP4A
Go to UniProtKB:  P19156
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase subunit beta
B, F
289Sus scrofaMutation(s): 0 
Gene Names: ATP4B
Find proteins for P18434 (Sus scrofa)
Go to Gene View: ATP4B
Go to UniProtKB:  P18434
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

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

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

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

Download SDF File 
Download CCD File 
A, F
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.263 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 191.510α = 90.00
b = 106.430β = 107.79
c = 250.960γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-09-04
    Type: Data collection, Database references