4UX1

Cryo-EM structure of antagonist-bound E2P gastric H,K-ATPase (SCH.E2. AlF)

Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 8.00 Å
  • R-Value Free: 0.516 
  • R-Value Work: 0.507 
  • R-Value Observed: 0.507 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating.

Abe, K., Tani, K., Fujiyoshi, Y.

(2014) J Biol Chem 289: 30590

  • DOI: 10.1074/jbc.M114.584623
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Gastric H(+),K(+)-ATPase, an ATP-driven proton pump responsible for gastric acidification, is a molecular target for anti-ulcer drugs. Here we show its cryo-electron microscopy (EM) structure in an E2P analog state, bound to magnesium fluoride (MgF), ...

    Gastric H(+),K(+)-ATPase, an ATP-driven proton pump responsible for gastric acidification, is a molecular target for anti-ulcer drugs. Here we show its cryo-electron microscopy (EM) structure in an E2P analog state, bound to magnesium fluoride (MgF), and its K(+)-competitive antagonist SCH28080, determined at 7 Å resolution by electron crystallography of two-dimensional crystals. Systematic comparison with other E2P-related cryo-EM structures revealed that the molecular conformation in the (SCH)E2·MgF state is remarkably distinguishable. Although the azimuthal position of the A domain of the (SCH)E2·MgF state is similar to that in the E2·AlF (aluminum fluoride) state, in which the transmembrane luminal gate is closed, the arrangement of transmembrane helices in the (SCH)E2·MgF state shows a luminal-open conformation imposed on by bound SCH28080 at its luminal cavity, based on observations of the structure in the SCH28080-bound E2·BeF (beryllium fluoride) state. The molecular conformation of the (SCH)E2·MgF state thus represents a mixed overall structure in which its cytoplasmic and luminal half appear to be independently modulated by a phosphate analog and an antagonist bound to the respective parts of the enzyme. Comparison of the molecular conformations revealed that the linker region connecting the A domain and the transmembrane helix 2 (A-M2 linker) mediates the regulation of luminal gating. The mechanistic rationale underlying luminal gating observed in H(+),K(+)-ATPase is consistent with that observed in sarcoplasmic reticulum Ca(2+)-ATPase and other P-type ATPases and is most likely conserved for the P-type ATPase family in general.

    Organizational Affiliation: 

    From the Cellular and Structural Physiology Institute and Graduate School of Pharmaceutical Science, Nagoya University, Nagoya 464-8601, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
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
  • R-Value Free: 0.516 
  • R-Value Work: 0.507 
  • R-Value Observed: 0.507 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.9α = 90
b = 111.3β = 90
c = 320γ = 90
Software Package:
Software NamePurpose
MRCmodel building
CNSrefinement
MRCdata scaling
MRCphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2014-11-12
    Changes: Database references