4P6V

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

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:  
    4P6V, 4U9Q, 4U9S, 4U9U, 4U9O, 4UAJ

  • 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 pathogenic bacteria, consists of six subunits, NqrA, B, C, D, E and F ...

    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

    Institute for Neuropathology, University of Freiburg, Breisacher Strasse 64, 79106 Freiburg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit AA449Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: nqrAVC_2295
EC: 1.6.5 (PDB Primary Data), 7.2.1.1 (UniProt)
Find proteins for Q9KPS1 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
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Go to UniProtKB:  Q9KPS1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit BB415Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: nqrBVC_2294
EC: 1.6.5 (PDB Primary Data), 7.2.1.1 (UniProt)
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))
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Go to UniProtKB:  Q9KPS2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit CC257Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: nqrCVC_2293
EC: 1.6.5 (PDB Primary Data), 7.2.1.1 (UniProt)
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))
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Go to UniProtKB:  P0C6E0
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit DD210Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: nqrDVC_2292
EC: 1.6.5 (PDB Primary Data), 7.2.1.1 (UniProt)
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))
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Go to UniProtKB:  Q9X4Q6
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit EE198Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: nqrEVC_2291
EC: 1.6.5 (PDB Primary Data), 7.2.1.1 (UniProt)
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))
Explore Q9X4Q7 
Go to UniProtKB:  Q9X4Q7
Protein Feature View
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit FF408Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: nqrFVC_2290
EC: 1.6.5 (PDB Primary Data), 7.2.1.1 (UniProt)
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))
Explore Q9X4Q8 
Go to UniProtKB:  Q9X4Q8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
M [auth F]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FMN
Query on FMN

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G [auth B], H [auth C]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
RBF
Query on RBF

Download Ideal Coordinates CCD File 
K [auth E]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
L [auth F]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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J [auth D]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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I [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.35α = 90
b = 143.38β = 110.96
c = 104.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
DMphasing
XDSdata scaling
XSCALEdata scaling

Structure Validation

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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  (Full details and data files)

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