4CZB | pdb_00004czb

Structure of the sodium proton antiporter MjNhaP1 from Methanocaldococcus jannaschii at pH 8.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.302 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.252 (Depositor), 0.261 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 184.25 kDa 
  • Atom Count: 12,548 
  • Modeled Residue Count: 1,655 
  • Deposited Residue Count: 1,704 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NA(+)/H(+) ANTIPORTER 1
A, B, D
426Methanocaldococcus jannaschiiMutation(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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NA(+)/H(+) ANTIPORTER 1426Methanocaldococcus jannaschiiMutation(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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.302 (Depositor), 0.305 (DCC) 
  • R-Value Work:  0.252 (Depositor), 0.261 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.437α = 90
b = 102.544β = 105.63
c = 132.096γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

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: Data collection, Database references, Derived calculations, Other, Refinement description