2YN9

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


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 8.00 Å

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 U S A 109: 18401

  • DOI: 10.1073/pnas.1212294109
  • Primary Citation of Related Structures:  
    2YN9

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1A1034Sus scrofaMutation(s): 0 
Gene Names: ATP4A
EC: 3.6.3.10 (PDB Primary Data), 7.2.2.19 (UniProt)
Find proteins for P19156 (Sus scrofa)
Explore P19156 
Go to UniProtKB:  P19156
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETAB290Sus scrofaMutation(s): 0 
Gene Names: ATP4B
Find proteins for P18434 (Sus scrofa)
Explore P18434 
Go to UniProtKB:  P18434
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 8.00 Å
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141α = 90
b = 110.6β = 90
c = 320γ = 90
Software Package:
Software NamePurpose
MRCmodel building
SITUSrefinement
MRCdata scaling
MRCphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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