9IBX | pdb_00009ibx

Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in replication conformer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Modelling POLG mutations in mice unravels a critical role of POL gamma Beta in regulating phenotypic severity.

Corra, S.Zuppardo, A.Valenzuela, S.Jenninger, L.Cerutti, R.Sillamaa, S.Hoberg, E.Johansson, K.A.S.Rovsnik, U.Volta, S.Silva-Pinheiro, P.Davis, H.Trifunovic, A.Minczuk, M.Gustafsson, C.M.Suomalainen, A.Zeviani, M.Macao, B.Zhu, X.Falkenberg, M.Viscomi, C.

(2025) Nat Commun 16: 4782-4782

  • DOI: https://doi.org/10.1038/s41467-025-60059-y
  • Primary Citation of Related Structures:  
    9G74, 9G75, 9G77, 9IBX, 9IBZ, 9IC0, 9IC1, 9IC3

  • PubMed Abstract: 

    DNA polymerase γ (POLγ), responsible for mitochondrial DNA replication, consists of a catalytic POLγA subunit and two accessory POLγB subunits. Mutations in POLG, which encodes POLγA, lead to various mitochondrial diseases. We investigated the most common POLG mutations (A467T, W748S, G848S, Y955C) by characterizing human and mouse POLγ variants. Our data reveal that these mutations significantly impair POLγ activities, with mouse variants exhibiting milder defects. Cryogenic electron microscopy highlighted structural differences between human and mouse POLγ, particularly in the POLγB subunit, which may explain the higher activity of mouse POLγ and the reduced severity of mutations in mice. We further generated a panel of mouse models mirroring common human POLG mutations, providing crucial insights into the pathogenesis of POLG-related disorders and establishing robust models for therapeutic development. Our findings emphasize the importance of POLγB in modulating the severity of POLG mutations.


  • Organizational Affiliation

    Veneto Institute of Molecular Medicine (VIMM), Via Orus, 2-35129, Padova, Italy.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-11,199Mus musculusMutation(s): 0 
Gene Names: Polg
EC: 2.7.7.7
UniProt
Find proteins for Q75WC0 (Mus musculus)
Explore Q75WC0 
Go to UniProtKB:  Q75WC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75WC0
Sequence Annotations
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  • Reference Sequence
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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
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (primer strand)D [auth P]25synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (template strand)E [auth T]40synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release