5BZ3

CRYSTAL STRUCTURE OF SODIUM PROTON ANTIPORTER NAPA IN OUTWARD-FACING CONFORMATION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.206 

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:  

  • 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 ...

    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.,Center for Biological Physics, Arizona State University, Tempe, Arizona, USA.,Department of Physics, Arizona State University, Tempe, Arizona, USA.,School of Life Sciences, University of Warwick, Coventry, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Na(+)/H(+) antiporter
A
385Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Antiporters
Protein: 
NapA Na+/H+ antiporter
Find proteins for Q5SIA2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIA2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7E8
Query on 7E8

Download SDF File 
Download CCD File 
A
(2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE
7.7 MAG
C17 H32 O4
LVBAGTJIDOCNIJ-XITLMJRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 56.580α = 90.00
b = 94.090β = 90.00
c = 147.280γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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