4UAJ

Crystal structure of NqrF in hexagonal space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7019 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the V. cholerae Na+-pumping NADH:quinone oxidoreductase.

Steuber, J.Vohl, G.Casutt, M.S.Vorburger, T.Diederichs, K.Fritz, G.

(2014) Nature 516: 62-67

  • DOI: 10.1038/nature14003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NADH oxidation in the respiratory chain is coupled to ion translocation across the membrane to build up an electrochemical gradient. The sodium-translocating NADH:quinone oxidoreductase (Na(+)-NQR), a membrane protein complex widespread among pathoge ...

    NADH oxidation in the respiratory chain is coupled to ion translocation across the membrane to build up an electrochemical gradient. The sodium-translocating NADH:quinone oxidoreductase (Na(+)-NQR), a membrane protein complex widespread among pathogenic bacteria, consists of six subunits, NqrA, B, C, D, E and F. To our knowledge, no structural information on the Na(+)-NQR complex has been available until now. Here we present the crystal structure of the Na(+)-NQR complex at 3.5 Å resolution. The arrangement of cofactors both at the cytoplasmic and the periplasmic side of the complex, together with a hitherto unknown iron centre in the midst of the membrane-embedded part, reveals an electron transfer pathway from the NADH-oxidizing cytoplasmic NqrF subunit across the membrane to the periplasmic NqrC, and back to the quinone reduction site on NqrA located in the cytoplasm. A sodium channel was localized in subunit NqrB, which represents the largest membrane subunit of the Na(+)-NQR and is structurally related to urea and ammonia transporters. On the basis of the structure we propose a mechanism of redox-driven Na(+) translocation where the change in redox state of the flavin mononucleotide cofactor in NqrB triggers the transport of Na(+) through the observed channel.


    Organizational Affiliation

    1] Institute for Neuropathology, University of Freiburg, Breisacher Strasse 64, 79106 Freiburg, Germany [2] Hermann-Staudinger-Graduate school, University of Freiburg, Hebelstrasse 27, 79104 Freiburg, Germany.,Institute for Neuropathology, University of Freiburg, Breisacher Strasse 64, 79106 Freiburg, Germany.,Department of Microbiology, Garbenstrasse 30, University of Hohenheim, 70599 Stuttgart, Germany.,Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Na(+)-translocating NADH-quinone reductase subunit F
A
284Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)Mutation(s): 0 
Gene Names: nqrF
EC: 7.2.1.1
Find proteins for A5F5Y4 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Go to UniProtKB:  A5F5Y4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7019 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 145.220α = 90.00
b = 145.220β = 90.00
c = 90.100γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-08-10 
  • Released Date: 2015-08-05 
  • Deposition Author(s): Fritz, G.

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Data collection, Experimental preparation