4GAV

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with quinone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.

Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A.D., Maher, M.J.

(2012) Proc Natl Acad Sci U S A 109: 15247-15252

  • DOI: 10.1073/pnas.1210059109
  • Primary Citation of Related Structures:  
    4G9K, 4GAV, 4GAP

  • PubMed Abstract: 

    • Bioenergy is efficiently produced in the mitochondria by the respiratory system consisting of complexes I-V. In various organisms, complex I can be replaced by the alternative NADH-quinone oxidoreductase (NDH-2), which catalyzes the transfer of an el ...

    Bioenergy is efficiently produced in the mitochondria by the respiratory system consisting of complexes I-V. In various organisms, complex I can be replaced by the alternative NADH-quinone oxidoreductase (NDH-2), which catalyzes the transfer of an electron from NADH via FAD to quinone, without proton pumping. The Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, directed to the matrix. A number of studies have investigated the potential use of Ndi1 as a therapeutic agent against complex I disorders, and the NDH-2 enzymes have emerged as potential therapeutic targets for treatments against the causative agents of malaria and tuberculosis. Here we present the crystal structures of Ndi1 in its substrate-free, NAD(+)- and ubiquinone- (UQ2) complexed states. The structures reveal that Ndi1 is a peripheral membrane protein forming an intimate dimer, in which packing of the monomeric units within the dimer creates an amphiphilic membrane-anchor domain structure. Crucially, the structures of the Ndi1-NAD(+) and Ndi1-UQ2 complexes show overlapping binding sites for the NAD(+) and quinone substrates.

    Organizational Affiliation: 

    Division of Molecular Biosciences, Imperial College, London, United Kingdom.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rotenone-insensitive NADH-ubiquinone oxidoreductaseA, B471Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NDI1, YML120C, YM7056.06C
EC: 1.6.5.9
Membrane protein
Mpstruc		Group: 
MONOTOPIC MEMBRANE PROTEINS		Sub Group: 
Dehydrogenases		Protein: 
Ndi1 NADH Dehydrogenase
Find proteins for P32340 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32340 
Go to UniProtKB:  P32340
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
UQ2
Query on UQ2
Download CCD File 
A, B
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.589α = 90
b = 111.926β = 90
c = 165.525γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references