5KSD

Crystal Structure of a Plasma Membrane Proton Pump


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.289 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Improved Model of Proton Pump Crystal Structure Obtained by Interactive Molecular Dynamics Flexible Fitting Expands the Mechanistic Model for Proton Translocation in P-Type ATPases.

Focht, D.Croll, T.I.Pedersen, B.P.Nissen, P.

(2017) Front Physiol 8: 202-202

  • DOI: 10.3389/fphys.2017.00202
  • Primary Citation of Related Structures:  
    5KSD

  • PubMed Abstract: 
  • The plasma membrane H + -ATPase is a proton pump of the P-type ATPase family and essential in plants and fungi. It extrudes protons to regulate pH and maintains a strong proton-motive force that energizes e.g., secondary uptake of nutrients. The only crystal structure of a H + -ATPase (AHA2 from Arabidopsis thaliana ) was reported in 2007 ...

    The plasma membrane H + -ATPase is a proton pump of the P-type ATPase family and essential in plants and fungi. It extrudes protons to regulate pH and maintains a strong proton-motive force that energizes e.g., secondary uptake of nutrients. The only crystal structure of a H + -ATPase (AHA2 from Arabidopsis thaliana ) was reported in 2007. Here, we present an improved atomic model of AHA2, obtained by a combination of model rebuilding through interactive molecular dynamics flexible fitting (iMDFF) and structural refinement based on the original data, but using up-to-date refinement methods. More detailed map features prompted local corrections of the transmembrane domain, in particular rearrangement of transmembrane helices 7 and 8, and the cytoplasmic N- and P-domains, and the new model shows improved overall quality and reliability scores. The AHA2 structure shows similarity to the Ca 2+ -ATPase E1 state, and provides a valuable starting point model for structural and functional analysis of proton transport mechanism of P-type H + -ATPases. Specifically, Asp684 protonation associated with phosphorylation and occlusion of the E1P state may result from hydrogen bond interaction with Asn106. A subsequent deprotonation associated with extracellular release in the E2P state may result from an internal salt bridge formation to an Arg655 residue, which in the present E1 state is stabilized in a solvated pocket. A release mechanism based on an in-built counter-cation was also later proposed for Zn 2+ -ATPase, for which structures have been determined in Zn 2+ released E2P-like states with the salt bridge interaction formed.


    Related Citations: 
    • Crystal structure of the plasma membrane proton pump.
      Pedersen, B.P., Buch-Pedersen, M.J., Morth, J.P., Palmgren, M.G., Nissen, P.
      (2007) Nature 450: 1111

    Organizational Affiliation

    PUMPkin, Danish National Research Foundation, Aarhus UniversityAarhus, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase 2, plasma membrane-typeA, B833Arabidopsis thalianaMutation(s): 0 
Gene Names: AHA2At4g30190F9N11.40
EC: 3.6.3.6 (PDB Primary Data), 7.1.2.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P19456 (Arabidopsis thaliana)
Explore P19456 
Go to UniProtKB:  P19456
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.289 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.29α = 90
b = 144.42β = 90
c = 312.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
autoSHARPphasing
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2017-05-17
    Changes: Database references