6HL3

wild-type NuoEF from Aquifex aeolicus - oxidized form bound to NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I.

Schulte, M.Frick, K.Gnandt, E.Jurkovic, S.Burschel, S.Labatzke, R.Aierstock, K.Fiegen, D.Wohlwend, D.Gerhardt, S.Einsle, O.Friedrich, T.

(2019) Nat Commun 10: 2551-2551

  • DOI: https://doi.org/10.1038/s41467-019-10429-0
  • Primary Citation of Related Structures:  
    6HL2, 6HL3, 6HL4, 6HLA, 6HLI, 6HLJ, 6HLM, 6Q9C, 6Q9G, 6Q9J, 6Q9K, 6R7P

  • PubMed Abstract: 

    Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. In humans its dysfunction is associated with degenerative diseases. Here we report the structure of the electron input part of Aquifex aeolicus complex I at up to 1.8 Å resolution with bound substrates in the reduced and oxidized states. The redox states differ by the flip of a peptide bond close to the NADH binding site. The orientation of this peptide bond is determined by the reduction state of the nearby [Fe-S] cluster N1a. Fixation of the peptide bond by site-directed mutagenesis led to an inactivation of electron transfer and a decreased reactive oxygen species (ROS) production. We suggest the redox-gated peptide flip to represent a previously unrecognized molecular switch synchronizing NADH oxidation in response to the redox state of the complex as part of an intramolecular feed-back mechanism to prevent ROS production.


  • Organizational Affiliation

    Boehringer Ingelheim Pharma GmbH & Co. KG, Lead Identification and Optimization Sup, 88397, Biberach, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit E
A, C
160Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: 63363
EC: 1.6.5.11
UniProt
Find proteins for O66842 (Aquifex aeolicus (strain VF5))
Explore O66842 
Go to UniProtKB:  O66842
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66842
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit F
B, D
434Aquifex aeolicusMutation(s): 0 
Gene Names: nuoFaq_573
EC: 1.6.5.11
UniProt
Find proteins for O66841 (Aquifex aeolicus (strain VF5))
Explore O66841 
Go to UniProtKB:  O66841
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66841
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
J [auth B],
U [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
I [auth B],
T [auth D]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
H [auth B],
S [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MPO
Query on MPO

Download Ideal Coordinates CCD File 
M [auth B],
W [auth D]
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
E [auth A],
Q [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
N [auth B]
O [auth B]
P [auth B]
R [auth C]
G [auth A],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth B],
V [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.514α = 90
b = 115.759β = 90
c = 189.635γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyRTG 2202

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release