4P6V

Crystal structure of the Na+-translocating NADH: ubiquinone oxidoreductase from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 A
A
449Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: nqrA
EC: 7.2.1.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Na+-pumping NADH:quinone oxidoreductase (Na+-NQR)
Find proteins for Q9KPS1 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KPS1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Na(+)-translocating NADH-quinone reductase subunit B
B
415Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: nqrB
EC: 7.2.1.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Na+-pumping NADH:quinone oxidoreductase (Na+-NQR)
Find proteins for Q9KPS2 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KPS2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Na(+)-translocating NADH-quinone reductase subunit C
C
257Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: nqrC
EC: 7.2.1.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Na+-pumping NADH:quinone oxidoreductase (Na+-NQR)
Find proteins for P0C6E0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  P0C6E0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Na(+)-translocating NADH-quinone reductase subunit D
D
210Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: nqrD
EC: 7.2.1.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Na+-pumping NADH:quinone oxidoreductase (Na+-NQR)
Find proteins for Q9X4Q6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9X4Q6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Na(+)-translocating NADH-quinone reductase subunit E
E
198Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: nqrE
EC: 7.2.1.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Na+-pumping NADH:quinone oxidoreductase (Na+-NQR)
Find proteins for Q9X4Q7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9X4Q7
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Na(+)-translocating NADH-quinone reductase subunit F
F
408Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: nqrF
EC: 7.2.1.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
Na+-pumping NADH:quinone oxidoreductase (Na+-NQR)
Find proteins for Q9X4Q8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9X4Q8
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

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Download CCD File 
E
RIBOFLAVIN
RIBOFLAVINE; VITAMIN B2
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
FMN
Query on FMN

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Download CCD File 
B, C
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
F
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
F
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.350α = 90.00
b = 143.380β = 110.96
c = 104.490γ = 90.00
Software Package:
Software NamePurpose
DMphasing
XDSdata scaling
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bade-Wuerttemberg StiftungGermanyP-LS-Meth/4
German Research Foundation (DFG)GermanyFR 1488/3-2
German Research Foundation (DFG)GermanyFR 1321/3-1

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence