Crystal structure of human COQ9 in complex with a phospholipid, Northeast Structural Genomics Consortium Target HR5043

Experimental Data Snapshot

  • Resolution: 2.39 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis.

Lohman, D.C.Forouhar, F.Beebe, E.T.Stefely, M.S.Minogue, C.E.Ulbrich, A.Stefely, J.A.Sukumar, S.Luna-Sanchez, M.Jochem, A.Lew, S.Seetharaman, J.Xiao, R.Wang, H.Westphall, M.S.Wrobel, R.L.Everett, J.K.Mitchell, J.C.Lopez, L.C.Coon, J.J.Tong, L.Pagliarini, D.J.

(2014) Proc Natl Acad Sci U S A 111: E4697-E4705

  • DOI: https://doi.org/10.1073/pnas.1413128111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Coenzyme Q (CoQ) is an isoprenylated quinone that is essential for cellular respiration and is synthesized in mitochondria by the combined action of at least nine proteins (COQ1-9). Although most COQ proteins are known to catalyze modifications to CoQ precursors, the biochemical role of COQ9 remains unclear. Here, we report that a disease-related COQ9 mutation leads to extensive disruption of the CoQ protein biosynthetic complex in a mouse model, and that COQ9 specifically interacts with COQ7 through a series of conserved residues. Toward understanding how COQ9 can perform these functions, we solved the crystal structure of Homo sapiens COQ9 at 2.4 Å. Unexpectedly, our structure reveals that COQ9 has structural homology to the TFR family of bacterial transcriptional regulators, but that it adopts an atypical TFR dimer orientation and is not predicted to bind DNA. Our structure also reveals a lipid-binding site, and mass spectrometry-based analyses of purified COQ9 demonstrate that it associates with multiple lipid species, including CoQ itself. The conserved COQ9 residues necessary for its interaction with COQ7 comprise a surface patch around the lipid-binding site, suggesting that COQ9 might serve to present its bound lipid to COQ7. Collectively, our data define COQ9 as the first, to our knowledge, mammalian TFR structural homolog and suggest that its lipid-binding capacity and association with COQ7 are key features for enabling CoQ biosynthesis.

  • Organizational Affiliation

    Chemistry, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706 Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706;

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinone biosynthesis protein COQ9, mitochondrial
A, B
235Homo sapiensMutation(s): 0 
Gene Names: COQ9C16orf49HSPC326PSEC0129
UniProt & NIH Common Fund Data Resources
Find proteins for O75208 (Homo sapiens)
Explore O75208 
Go to UniProtKB:  O75208
PHAROS:  O75208
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75208
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEF

Download Ideal Coordinates CCD File 
C37 H74 N O8 P
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.39 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.34α = 90
b = 97.628β = 95.77
c = 64.109γ = 90
Software Package:
Software NamePurpose
RESOLVEmodel building
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Changes: Database references
  • Version 1.2: 2014-11-19
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection