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), 0.200 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view details

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 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 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), 0.200 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.170 (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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view details

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