8ACW | pdb_00008acw

X-ray structure of Na+-NQR from Vibrio cholerae at 3.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.306 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.270 (Depositor), 0.271 (DCC) 
  • R-Value Observed: 
    0.272 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8ACW

Ligand Structure Quality Assessment 


This is version 1.5 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: 217.76 kDa 
  • Atom Count: 14,308 
  • Modeled Residue Count: 1,833 
  • 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: nqrAERS013165_00619ERS013186_02081ERS013199_02394ERS013202_01882ERS013206_02986ERS013207_01957
EC: 7.2.1.1
UniProt
Find proteins for A5F5X1 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F5X1 
Go to UniProtKB:  A5F5X1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F5X1
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: 
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A5F5X0 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F5X0 
Go to UniProtKB:  A5F5X0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F5X0
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: 
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A5F5Y7 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F5Y7 
Go to UniProtKB:  A5F5Y7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F5Y7
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: 
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A5F5Y6 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F5Y6 
Go to UniProtKB:  A5F5Y6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F5Y6
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: 
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A5F5Y5 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F5Y5 
Go to UniProtKB:  A5F5Y5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F5Y5
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: nqrFD6U24_04485ERS013198_02504ERS013199_02399ERS013201_01113ERS013202_01887ERS013206_02991EYB64_17930FLM12_12900
EC: 7.2.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A5F5Y4 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F5Y4 
Go to UniProtKB:  A5F5Y4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F5Y4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
P [auth F]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
I [auth B],
L [auth D],
N [auth E]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
G [auth B],
K [auth C]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
RBF
(Subject of Investigation/LOI)

Query on RBF



Download:Ideal Coordinates CCD File
H [auth B]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
O [auth E],
Q [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
LYS

Query on LYS



Download:Ideal Coordinates CCD File
M [auth D]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
K

Query on K



Download:Ideal Coordinates CCD File
J [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.306 (Depositor), 0.305 (DCC) 
  • R-Value Work:  0.270 (Depositor), 0.271 (DCC) 
  • R-Value Observed: 0.272 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.72α = 90
b = 142.94β = 109.93
c = 103.39γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-07-12 
  • Deposition Author(s): Fritz, G.

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany311211092

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-27
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Database references
  • Version 1.4: 2024-02-07
    Changes: Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary