4CZ9 | pdb_00004cz9

Structure of the sodium proton antiporter PaNhaP from Pyrococcus abyssii at pH 4.

• PDB DOI: https://doi.org/10.2210/pdb4CZ9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2014-04-16 Released: 2014-12-17 
• Deposition Author(s): Woehlert, D., Kuhlbrandt, W., Yildiz, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.263 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.255 (DCC) 

Starting Model: experimental

Literature

Structure and substrate ion binding in the sodium/proton antiporter PaNhaP.

Wohlert, D., Kuhlbrandt, W., Yildiz, O.

(2014) Elife 3: e03579-e03579

• PubMed: 25426802 
• DOI: https://doi.org/10.7554/eLife.03579
• Primary Citation Related Structures: 
  4CZ8, 4CZ9, 4CZA


• PubMed Abstract: 
  

  Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed structures of antiporters with bound substrate ions are essential for understanding how they work. We have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2 Å, and have determined its structure in two different conformations at pH 8 and pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface. Combined with comprehensive transport studies, the structures of PaNhaP offer unique new insights into the transport mechanism of sodium/proton antiporters.

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Organizational Affiliation: 
• Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.61 kDa 
• Atom Count: 6,592 
• Modeled Residue Count: 839 
• Deposited Residue Count: 844 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NA+/H+ ANTIPORTER, PUTATIVE	A, B	422	Pyrococcus abyssi GE5	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9UZ55 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9UZ55  Go to UniProtKB:  Q9UZ55

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OOC	C [auth B]	octyl 4-O-beta-D-allopyranosyl-1-thio-beta-D-altropyranoside C20 H38 O10 S JHBBNAKIOKQRJS-AIIAIXEESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.263 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.255 (DCC) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.566	α = 90
b = 109.566	β = 90
c = 209.626	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Woehlert, D., Kuhlbrandt, W., Yildiz, O.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2019-02-27
  Changes: Data collection, Database references, Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description