6AWL | pdb_00006awl

Crystal structure of human Coq9

• PDB DOI: https://doi.org/10.2210/pdb6AWL/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-05 Released: 2019-02-06 
• Deposition Author(s): Bingman, C.A., Lohman, D.C., Smith, R.W., Pagliarini, D.J., Mitochondrial Protein Partnership (MPP)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis.

Lohman, D.C., Aydin, D., Von Bank, H.C., Smith, R.W., Linke, V., Weisenhorn, E., McDevitt, M.T., Hutchins, P., Wilkerson, E.M., Wancewicz, B., Russell, J., Stefely, M.S., Beebe, E.T., Jochem, A., Coon, J.J., Bingman, C.A., Dal Peraro, M., Pagliarini, D.J.

(2019) Mol Cell 73: 763

• PubMed: 30661980 
• DOI: https://doi.org/10.1016/j.molcel.2018.11.033
• Primary Citation Related Structures: 
  6AWL, 6DEW


• PubMed Abstract: 
  

  The biosynthesis of coenzyme Q presents a paradigm for how cells surmount hydrophobic barriers in lipid biology. In eukaryotes, CoQ precursors-among nature's most hydrophobic molecules-must somehow be presented to a series of enzymes peripherally associated with the mitochondrial inner membrane. Here, we reveal that this process relies on custom lipid-binding properties of COQ9. We show that COQ9 repurposes the bacterial TetR fold to bind aromatic isoprenes with high specificity, including CoQ intermediates that likely reside entirely within the bilayer. We reveal a process by which COQ9 associates with cardiolipin-rich membranes and warps the membrane surface to access this cargo. Finally, we identify a molecular interface between COQ9 and the hydroxylase COQ7, motivating a model whereby COQ9 presents intermediates directly to CoQ enzymes. Overall, our results provide a mechanism for how a lipid-binding protein might access, select, and deliver specific cargo from a membrane to promote biosynthesis.

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Organizational Affiliation: 
• Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53715, USA.
Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
Morgridge Institute for Research, Madison, WI 53715, USA.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53715, USA.
Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA.
Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA.
Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA; Genome Center of Wisconsin, Madison, WI 53715, USA.
Morgridge Institute for Research, Madison, WI 53715, USA; Genome Center of Wisconsin, Madison, WI 53715, USA.
Morgridge Institute for Research, Madison, WI 53715, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA; Genome Center of Wisconsin, Madison, WI 53715, USA.
Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. Electronic address: [e-mail].
Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53715, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72 kDa 
• Atom Count: 3,564 
• Modeled Residue Count: 408 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinone biosynthesis protein COQ9, mitochondrial	A, B	318	Homo sapiens	Mutation(s): 0  Gene Names: COQ9, C16orf49, HSPC326, PSEC0129
UniProt & NIH Common Fund Data Resources
Find proteins for O75208 (Homo sapiens) Explore O75208  Go to UniProtKB:  O75208
PHAROS:  O75208 GTEx:  ENSG00000088682

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEF	C [auth A]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C37 H74 N O8 P SLKDGVPOSSLUAI-PGUFJCEWSA-N
BTB	D [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.11	α = 90
b = 97.39	β = 95.4
c = 63.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Bingman, C.A., Lohman, D.C., Smith, R.W., Pagliarini, D.J., Mitochondrial Protein Partnership (MPP)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1U01GM094622-01

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-03-06
  Changes: Data collection, Database references
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description