2YN9

Cryo-EM structure of gastric H+,K+-ATPase with bound rubidium


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 8 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-Em Structure of Gastric H+,K+-ATPase with a Single Occupied Cation-Binding Site.

Abe, K.Tani, K.Friedrich, T.Fujiyoshi, Y.

(2012) Proc.Natl.Acad.Sci.USA 109: 18401

  • DOI: 10.1073/pnas.1212294109

  • PubMed Abstract: 
  • Gastric H(+),K(+)-ATPase is responsible for gastric acid secretion. ATP-driven H(+) uptake into the stomach is efficiently accomplished by the exchange of an equal amount of K(+), resulting in a luminal pH close to 1. Because of the limited free ener ...

    Gastric H(+),K(+)-ATPase is responsible for gastric acid secretion. ATP-driven H(+) uptake into the stomach is efficiently accomplished by the exchange of an equal amount of K(+), resulting in a luminal pH close to 1. Because of the limited free energy available for ATP hydrolysis, the stoichiometry of transported cations is thought to vary from 2H(+)/2K(+) to 1H(+)/1K(+) per hydrolysis of one ATP molecule as the luminal pH decreases, although direct evidence for this hypothesis has remained elusive. Here, we show, using the phosphate analog aluminum fluoride (AlF) and a K(+) congener (Rb(+)), the 8-Å resolution structure of H(+),K(+)-ATPase in the transition state of dephosphorylation, (Rb(+))E2~AlF, which is distinct from the preceding Rb(+)-free E2P state. A strong density located in the transmembrane cation-binding site of (Rb(+))E2~AlF highly likely represents a single bound Rb(+) ion, which is clearly different from the Rb(+)-free E2AlF or K(+)-bound (K(+))E2~AlF structures. Measurement of radioactive (86)Rb(+) binding suggests that the binding stoichiometry varies depending on the pH, and approximately half of the amount of Rb(+) is bound under acidic crystallization conditions compared with at a neutral pH. These data represent structural and biochemical evidence for the 1H(+)/1K(+)/1ATP transport mode of H(+),K(+)-ATPase, which is a prerequisite for generation of the 10(6)-fold proton gradient in terms of thermodynamics. Together with the released E2P-stabilizing interaction between the β subunit's N terminus and the P domain observed in the (Rb(+))E2~AlF structure, we propose a refined vectorial transport model of H(+),K(+)-ATPase, which must prevail against the highly acidic state of the gastric lumen.


    Organizational Affiliation

    Cellular and Structural Physiology Institute, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan. kabe@cespi.nagoya-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1
A
1034Sus scrofaGene Names: ATP4A
EC: 3.6.3.10
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
290Sus scrofaGene Names: ATP4B
Find proteins for P18434 (Sus scrofa)
Go to Gene View: ATP4B
Go to UniProtKB:  P18434
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 8 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 
Software Package:
Software NamePurpose
MRCphasing
MRCdata scaling
SITUSrefinement
MRCmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-01-16
    Type: Database references, Derived calculations, Other
  • Version 1.2: 2014-07-16
    Type: Other