5BZ2

CRYSTAL STRUCTURE OF THE SODIUM PROTON ANTIPORTER NAPA IN INWARD-FACING CONFORMATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.294 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters.

Coincon, M.Uzdavinys, P.Nji, E.Dotson, D.L.Winkelmann, I.Abdul-Hussein, S.Cameron, A.D.Beckstein, O.Drew, D.

(2016) Nat Struct Mol Biol 23: 248-255

  • DOI: 10.1038/nsmb.3164
  • Primary Citation of Related Structures:  
    5BZ2, 5BZ3

  • PubMed Abstract: 
  • To fully understand the transport mechanism of Na(+)/H(+) exchangers, it is necessary to clearly establish the global rearrangements required to facilitate ion translocation. Currently, two different transport models have been proposed. Some reports have suggested that structural isomerization is achieved through large elevator-like rearrangements similar to those seen in the structurally unrelated sodium-coupled glutamate-transporter homolog GltPh ...

    To fully understand the transport mechanism of Na(+)/H(+) exchangers, it is necessary to clearly establish the global rearrangements required to facilitate ion translocation. Currently, two different transport models have been proposed. Some reports have suggested that structural isomerization is achieved through large elevator-like rearrangements similar to those seen in the structurally unrelated sodium-coupled glutamate-transporter homolog GltPh. Others have proposed that only small domain movements are required for ion exchange, and a conventional rocking-bundle model has been proposed instead. Here, to resolve these differences, we report atomic-resolution structures of the same Na(+)/H(+) antiporter (NapA from Thermus thermophilus) in both outward- and inward-facing conformations. These data combined with cross-linking, molecular dynamics simulations and isothermal calorimetry suggest that Na(+)/H(+) antiporters provide alternating access to the ion-binding site by using elevator-like structural transitions.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)/H(+) antiporterA386Thermus thermophilusMutation(s): 2 
Gene Names: TT_C1108
Membrane Entity: Yes 
UniProt
Find proteins for Q5SIA2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIA2 
Go to UniProtKB:  Q5SIA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIA2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.294 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.71α = 90
b = 84.64β = 90
c = 201.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references, Structure summary
  • Version 1.2: 2016-02-03
    Changes: Database references
  • Version 1.3: 2016-02-10
    Changes: Database references
  • Version 1.4: 2016-03-09
    Changes: Database references