6JXJ

Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 1A987Sus scrofaMutation(s): 4 
Gene Names: ATP4A
EC: 7.2.2.19
Find proteins for P19156 (Sus scrofa)
Explore P19156 
Go to UniProtKB:  P19156
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase subunit betaB289Sus 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
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download CCD File 
A
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
CE1
Query on CE1

Download CCD File 
A
O-DODECANYL OCTAETHYLENE GLYCOL
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N
 Ligand Interaction
CLR
Query on CLR

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

Download CCD File 
B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ALF
Query on ALF

Download CCD File 
A
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
RB
Query on RB

Download CCD File 
A, B
RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.23α = 90
b = 103.23β = 90
c = 369.44γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-04-23 
  • Released Date: 2019-08-14 
  • Deposition Author(s): Abe, K., Irie, K.

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary