6JXK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.267 

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
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 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.



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 UniProtKB:  P19156

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  P18434
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

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

Download CCD File 
B, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MF4
Query on MF4

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

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

Download CCD File 
A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.267 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.51α = 90
b = 106.43β = 107.79
c = 250.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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