8A1U

Sodium pumping NADH-quinone oxidoreductase with substrates NADH and Q2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conformational coupling of redox-driven Na + -translocation in Vibrio cholerae NADH:quinone oxidoreductase.

Hau, J.L.Kaltwasser, S.Muras, V.Casutt, M.S.Vohl, G.Claussen, B.Steffen, W.Leitner, A.Bill, E.Cutsail 3rd, G.E.DeBeer, S.Vonck, J.Steuber, J.Fritz, G.

(2023) Nat Struct Mol Biol 30: 1686-1694

  • DOI: https://doi.org/10.1038/s41594-023-01099-0
  • Primary Citation of Related Structures:  
    8A1T, 8A1U, 8A1V, 8A1W, 8A1X, 8A1Y, 8ACW, 8ACY, 8AD3, 8AD4, 8AD5

  • PubMed Abstract: 

    In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH:quinone oxidoreductase (Na + -NQR) generates a sodium gradient by a so far unknown mechanism. Here we show that ion pumping in Na + -NQR is driven by large conformational changes coupling electron transfer to ion translocation. We have determined a series of cryo-EM and X-ray structures of the Na + -NQR that represent snapshots of the catalytic cycle. The six subunits NqrA, B, C, D, E, and F of Na + -NQR harbor a unique set of cofactors that shuttle the electrons from NADH twice across the membrane to quinone. The redox state of a unique intramembranous [2Fe-2S] cluster orchestrates the movements of subunit NqrC, which acts as an electron transfer switch. We propose that this switching movement controls the release of Na + from a binding site localized in subunit NqrB.


  • Organizational Affiliation

    Department of Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit A468Vibrio choleraeMutation(s): 0 
Gene Names: nqrAVC_2295
EC: 7.2.1.1
UniProt
Find proteins for Q9KPS1 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KPS1 
Go to UniProtKB:  Q9KPS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KPS1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit B415Vibrio choleraeMutation(s): 0 
Gene Names: nqrBVC_2294
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9KPS2 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KPS2 
Go to UniProtKB:  Q9KPS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KPS2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit C257Vibrio choleraeMutation(s): 0 
Gene Names: nqrCVC_2293
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0C6E0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P0C6E0 
Go to UniProtKB:  P0C6E0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6E0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit D210Vibrio choleraeMutation(s): 0 
Gene Names: nqrDVC_2292
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9X4Q6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9X4Q6 
Go to UniProtKB:  Q9X4Q6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X4Q6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit E198Vibrio choleraeMutation(s): 0 
Gene Names: nqrEVC_2291
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9X4Q7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9X4Q7 
Go to UniProtKB:  Q9X4Q7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X4Q7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit F408Vibrio choleraeMutation(s): 0 
Gene Names: nqrFVC_2290
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9X4Q8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9X4Q8 
Go to UniProtKB:  Q9X4Q8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X4Q8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
U [auth F]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
J [auth B],
L [auth B],
N [auth B],
R [auth D]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NAI
Query on NAI

Download Ideal Coordinates CCD File 
W [auth F]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
I [auth B],
K [auth B],
S [auth D]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
G [auth B],
Q [auth C]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
RBF
Query on RBF

Download Ideal Coordinates CCD File 
H [auth B]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
UQ2
Query on UQ2

Download Ideal Coordinates CCD File 
M [auth B]UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
T [auth E],
V [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth B],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFR 1488/8-2

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Database references