4D0A

3D EM map of the sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 6.00 Å

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

3D Em Map of the Sodium Proton Antiporter Mjnhap1 from Methanocaldococcus Jannaschii

Paulino, C.Woehlert, D.Yildiz, O.Kuhlbrandt, W.

(2014) Elife 3

  • DOI: https://doi.org/10.7554/eLife.03583
  • Primary Citation of Related Structures:  
    4CZB, 4D0A

  • PubMed Abstract: 

    Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 in two complementary states. The inward-open state was obtained by x-ray crystallography in the presence of sodium at pH 8, where the transporter is highly active. The outward-open state was obtained by electron crystallography without sodium at pH 4, where MjNhaP1 is inactive. Comparison of both structures reveals a 7° tilt of the 6 helix bundle. (22)Na(+) uptake measurements indicate non-cooperative transport with an activity maximum at pH 7.5. We conclude that binding of a Na(+) ion from the outside induces helix movements that close the extracellular cavity, open the cytoplasmic funnel, and result in a ∼5 Å vertical relocation of the ion binding site to release the substrate ion into the cytoplasm.


  • Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NA(+)/H(+) ANTIPORTER 1A [auth B]426Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q60362 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q60362 
Go to UniProtKB:  Q60362
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60362
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 6.00 Å
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.5α = 90
b = 103.3β = 90
c = 200γ = 90
Software Package:
Software NamePurpose
2DXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Author supporting evidence, Data collection, Database references, Refinement description