8A1V

Sodium pumping NADH-quinone oxidoreductase with substrate Q2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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. guenter.fritz@uni-hohenheim.de.


Macromolecules
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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
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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))
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Go to UniProtKB:  A5F5X0
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F5X0
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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))
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UniProt GroupA5F5Y7
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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))
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Go to UniProtKB:  A5F5Y6
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UniProt GroupA5F5Y6
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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
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UniProt GroupA5F5Y5
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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
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UniProt GroupA5F5Y4
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

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

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

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

Download Ideal Coordinates CCD File 
G [auth B]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
UQ2 (Subject of Investigation/LOI)
Query on UQ2

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

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

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M [auth B],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 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: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-09-27
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Database references