Skip to main content

 8A1U | pdb_00008a1u

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 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8A1U

This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 221.6 kDa 
  • Atom Count: 15,258 
  • Modeled Residue Count: 1,898 
  • Deposited Residue Count: 1,956 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit A468Vibrio choleraeMutation(s): 0 
Gene Names: nqrA, VC_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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit B415Vibrio choleraeMutation(s): 0 
Gene Names: nqrB, VC_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:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit C257Vibrio choleraeMutation(s): 0 
Gene Names: nqrC, VC_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:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit D210Vibrio choleraeMutation(s): 0 
Gene Names: nqrD, VC_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:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit E198Vibrio choleraeMutation(s): 0 
Gene Names: nqrE, VC_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:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit F408Vibrio choleraeMutation(s): 0 
Gene Names: nqrF, VC_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
  • Version 1.3: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.4: 2026-09-02
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Structure summary