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

---

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., Mattevi, A.

To be published.

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.

---

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