8AD3 | pdb_00008ad3

X-ray structure of NqrF(129-408)of Vibrio cholerae variant F406A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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: 65.5 kDa 
  • Atom Count: 5,056 
  • Modeled Residue Count: 556 
  • Deposited Residue Count: 562 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+)-translocating NADH-quinone reductase subunit F
A, B
281Vibrio choleraeMutation(s): 1 
Gene Names: nqrFERS013200_03807
EC: 7.2.1.1
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.54α = 90
b = 89.49β = 90
c = 89.59γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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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