9IBZ | pdb_00009ibz

Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in human-like error-editing conformer (composite)

• PDB DOI: https://doi.org/10.2210/pdb9IBZ/pdb
• NAKB: 9IBZ
• EM Map EMD-52819: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Mus musculus, Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2025-02-14 Released: 2025-06-04 
• Deposition Author(s): Valenzuela, S., Falkenberg, M.
• Funding Organization(s): Swedish Research Council, Cancerfonden, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 40404629 
• DOI: https://doi.org/10.1038/s41467-025-60059-y
• Primary Citation 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.

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Organizational Affiliation: 
• Veneto Institute of Molecular Medicine (VIMM), Via Orus, 2-35129, Padova, Italy.
Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B-35131, Padova, Italy.
Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A, P.O. Box 440, 41390, Gothenburg, Sweden.
MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK.
The Mary Lyon Centre, MRC Harwell, Becquerel Ave, Didcot, Oxfordshire, OX11 0RD, UK.
Institute for Mitochondrial Diseases and Aging, Faculty of Medicine, CECAD Research Center, 50931, Cologne, Germany.
Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 2PY, UK.
Research Programs Unit, Stem Cells and Metabolism, Biomedicum-Helsinki, Haartmaninkatu 8, University of Helsinki, 00290, Helsinki, Finland.
HUSlab, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland.
Department of Neurosciences, University of Padova, Via Belzoni 160, 35121, Padova, Italy.
Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Via Istria 61, 34137, Trieste, Italy.
Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A, P.O. Box 440, 41390, Gothenburg, Sweden. [e-mail].
School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, 063210, China. [e-mail].
National Key Laboratory for Development and Utilization of Forest Food Resources, Zhejiang A&F University, Hangzhou, 311300, China. [e-mail].
Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A, P.O. Box 440, 41390, Gothenburg, Sweden. [e-mail].
Veneto Institute of Molecular Medicine (VIMM), Via Orus, 2-35129, Padova, Italy. [e-mail].
Department of Biomedical Sciences, University of Padova, Via Ugo Bassi, 58/B-35131, Padova, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 262.03 kDa 
• Atom Count: 14,339 
• Modeled Residue Count: 1,721 
• Deposited Residue Count: 2,198 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase subunit gamma-1	A	1,199	Mus musculus	Mutation(s): 0  Gene Names: Polg EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt), 4.2.99 (UniProt)
UniProt
Find proteins for P54099 (Mus musculus) Explore P54099  Go to UniProtKB:  P54099

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase subunit gamma-2	B, C	467	Homo sapiens	Mutation(s): 1  Gene Names: POLG2, MTPOLB
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHN1 (Homo sapiens) Explore Q9UHN1  Go to UniProtKB:  Q9UHN1
PHAROS:  Q9UHN1 GTEx:  ENSG00000256525

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (primer strand)	D [auth P]	25	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (template strand)	E [auth T]	40	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP (Subject of Investigation/LOI)	G [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
CA (Subject of Investigation/LOI)	F [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Valenzuela, S., Falkenberg, M.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--
Cancerfonden	Sweden	--
Knut and Alice Wallenberg Foundation	Sweden	--

Revision History  

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