9TVN | pdb_00009tvn

Structure of the Tetrapod Ancestor COQ8A in complex with AMP-PNP and 2Mn(II)

• PDB DOI: https://doi.org/10.2210/pdb9TVN/pdb

• Classification: LIPID TRANSPORT
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-01-12 Released: 2026-06-24 
• Deposition Author(s): Gottinger, A., Mattevi, A.
• Funding Organization(s): European Research Council (ERC), Italian Association for Cancer Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.255 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.195 (DCC) 

Starting Model: in silico

Literature

COQ8 chaperones coenzyme Q lipid intermediates through ATP-driven structural gating.

Gottinger, A., Malatesta, M., Nicoll, C.R., Ansari, G., Quinodoz, M., Kaminska, K., Tang, R.W.C., Tan, T.E., Fenner, B.J., Barberan-Martinez, P., Garcia-Garcia, G., Millan, J.M., Pfau, M., Burbach, N.E., Cecchini, D., Rivolta, C., Mattevi, A.

(2026) Sci Adv 12: eaeg1124-eaeg1124

• PubMed: 42525751 
• DOI: https://doi.org/10.1126/sciadv.aeg1124
• Primary Citation Related Structures: 
  9TVK, 9TVN


• PubMed Abstract: 
  

  Coenzyme Q biosynthesis requires two atypical kinase-like proteins (COQ8A and COQ8B), whose detailed molecular mechanism remains unclear. Here, we show that both paralogs function as adenosine triphosphatases (ATPases) that promote coenzyme Q biosynthetic metabolon activity by engaging in loose protein-protein interactions and delivering insoluble biosynthetic intermediates. Structural bioinformatics and pathological variant-driven mutagenesis identify a previously uncharacterized pocket that selectively recognizes coenzyme Q biosynthetic intermediates via their head groups. X-ray crystallography reveals that access to this pocket is gated by long-range conformational changes controlled by adenosine 5'-triphosphate hydrolysis. Last, excess coenzyme Q suppresses binding of early-stage intermediates and thereby abolishes the promoting effect of COQ8 on the metabolon. Together, these findings support a model in which COQ8 tunes coenzyme Q biosynthesis by coupling ATPase-driven intermediate chaperoning to feedback inhibition by the final product.

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Organizational Affiliation: 
• Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, Via Ferrata 9, 27100 Pavia, Italy.
Department of Ophthalmology, University Hospital Basel, Basel, Switzerland.
Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.
Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore.
Duke-NUS Medical School, National University of Singapore, Singapore, Singapore.
Molecular, Cellular, and Genomic Biomedicine Group, Health Research Institute La Fe, Valencia, Spain.
Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
Department of Ophthalmology, University of Bonn, Bonn, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 56.67 kDa 
• Atom Count: 3,390 
• Modeled Residue Count: 391 
• Deposited Residue Count: 493 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Atypical kinase COQ8A, mitochondrial - reconstructed tetrapod ancestor	A	493	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.255 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.195 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.456	α = 90
b = 80.258	β = 90
c = 87.504	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-24 
Deposition Author(s): Gottinger, A., Mattevi, A.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101094471
Italian Association for Cancer Research	Italy	28754

Revision History  

• Version 1.0: 2026-06-24
  Type: Initial release
  
• Version 1.1: 2026-08-19
  Changes: Database references