9GGD | pdb_00009ggd

Structure of the A467T mutant of human mitochondrial DNA polymerase gamma in complex with PZL-A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Small molecules restore mutant mitochondrial DNA polymerase activity.

Valenzuela, S.Zhu, X.Macao, B.Stamgren, M.Geukens, C.Charifson, P.S.Kern, G.Hoberg, E.Jenninger, L.Gruszczyk, A.V.Lee, S.Johansson, K.A.S.Miralles Fuste, J.Shi, Y.Kerns, S.J.Arabanian, L.Martinez Botella, G.Ekstrom, S.Green, J.Griffin, A.M.Pardo-Hernandez, C.Keating, T.A.Kuppers-Munther, B.Larsson, N.G.Phan, C.Posse, V.Jones, J.E.Xie, X.Giroux, S.Gustafsson, C.M.Falkenberg, M.

(2025) Nature 642: 501-507

  • DOI: https://doi.org/10.1038/s41586-025-08856-9
  • Primary Citation of Related Structures:  
    9GGB, 9GGC, 9GGD, 9GGE, 9GGF

  • PubMed Abstract: 

    Mammalian mitochondrial DNA (mtDNA) is replicated by DNA polymerase γ (POLγ), a heterotrimeric complex consisting of a catalytic POLγA subunit and two accessory POLγB subunits 1 . More than 300 mutations in POLG, the gene encoding the catalytic subunit, have been linked to severe, progressive conditions with high rates of morbidity and mortality, for which no treatment exists 2 . Here we report on the discovery and characterization of PZL-A, a first-in-class small-molecule activator of mtDNA synthesis that is capable of restoring function to the most common mutant variants of POLγ. PZL-A binds to an allosteric site at the interface between the catalytic POLγA subunit and the proximal POLγB subunit, a region that is unaffected by nearly all disease-causing mutations. The compound restores wild-type-like activity to mutant forms of POLγ in vitro and activates mtDNA synthesis in cells from paediatric patients with lethal POLG disease, thereby enhancing biogenesis of the oxidative phosphorylation machinery and cellular respiration. Our work demonstrates that a small molecule can restore function to mutant DNA polymerases, offering a promising avenue for treating POLG disorders and other severe conditions linked to depletion of mtDNA.


  • Organizational Affiliation
    • Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-11,221Homo sapiensMutation(s): 1 
Gene Names: POLGMDP1POLG1POLGA
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P54098 (Homo sapiens)
Explore P54098 
Go to UniProtKB:  P54098
PHAROS:  P54098
GTEx:  ENSG00000140521 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54098
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-2
B, C
467Homo sapiensMutation(s): 1 
Gene Names: POLG2MTPOLB
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHN1 (Homo sapiens)
Explore Q9UHN1 
Go to UniProtKB:  Q9UHN1
PHAROS:  Q9UHN1
GTEx:  ENSG00000256525 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHN1
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (primer strand)D [auth P]25synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (template strand)E [auth T]40synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.3.1.

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden--
CancerfondenSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-25
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-02
    Changes: Data collection