7X20

Crystal structure of non gastric H,K-ATPase alpha2 in (K+)E2-AlF state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.267 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and function of H + /K + pump mutants reveal Na + /K + pump mechanisms.

Young, V.C.Nakanishi, H.Meyer, D.J.Nishizawa, T.Oshima, A.Artigas, P.Abe, K.

(2022) Nat Commun 13: 5270-5270

  • DOI: https://doi.org/10.1038/s41467-022-32793-0
  • Primary Citation of Related Structures:  
    7X20, 7X21, 7X22, 7X23, 7X24

  • PubMed Abstract: 

    Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na + to H + selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via P-type ATPases using functional and structural analyses to demonstrate that four simultaneous residue substitutions transform the non-gastric H + /K + pump, a strict H + -dependent electroneutral P-type ATPase, into a bona fide Na + -dependent electrogenic Na + /K + pump. Conversion of a H + -dependent primary-active transporter into a Na + -dependent one provides a prototype for similar studies of ion-transport proteins. Moreover, we solve the structures of the wild-type non-gastric H + /K + pump, a suitable drug target to treat cystic fibrosis, and of its Na + /K + pump-mimicking mutant in two major conformations, providing insight on how Na + binding drives a concerted mechanism leading to Na + /K + pump phosphorylation.


  • Organizational Affiliation

    Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium-transporting ATPase alpha chain 2986Rattus norvegicusMutation(s): 0 
Gene Names: Atp12aAtp1al1
EC: 7.2.2.19 (PDB Primary Data), 7.2.2.13 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P54708 (Rattus norvegicus)
Explore P54708 
Go to UniProtKB:  P54708
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54708
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1324Rattus norvegicusMutation(s): 0 
Gene Names: Atp1b1
Membrane Entity: Yes 
UniProt
Find proteins for P07340 (Rattus norvegicus)
Explore P07340 
Go to UniProtKB:  P07340
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07340
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P07340-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.267 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.97α = 90
b = 109.06β = 90
c = 267.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H02426

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description