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- PDB-9ibx: Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB... -

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Basic information

Entry
Database: PDB / ID: 9ibx
TitleChimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in replication conformer
Components
  • (DNA polymerase subunit gamma- ...) x 2
  • DNA (primer strand)
  • DNA (template strand)
KeywordsTRANSFERASE / Mitochondrial DNA polymerase
Function / homology
Function and homology information


gamma DNA polymerase complex / mitochondrial chromosome / mitochondrial DNA replication / Strand-asynchronous mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity ...gamma DNA polymerase complex / mitochondrial chromosome / mitochondrial DNA replication / Strand-asynchronous mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / DNA polymerase processivity factor activity / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / base-excision repair, gap-filling / DNA polymerase binding / Transcriptional activation of mitochondrial biogenesis / DNA-templated DNA replication / protease binding / double-stranded DNA binding / in utero embryonic development / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / chromatin binding / mitochondrion / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / POLG2, C-terminal / : / DNA mitochondrial polymerase exonuclease domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / DNA-directed DNA polymerase, family A, conserved site ...DNA-directed DNA-polymerase, family A, mitochondria / DNA mitochondrial polymerase, exonuclease domain / POLG2, C-terminal / : / DNA mitochondrial polymerase exonuclease domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase subunit gamma-1 / DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsValenzuela, S. / Falkenberg, M.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Cancerfonden Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2025
Title: Modelling POLG mutations in mice unravels a critical role of POLγΒ in regulating phenotypic severity.
Authors: Samantha Corrà / Alessandro Zuppardo / Sebastian Valenzuela / Louise Jenninger / Raffaele Cerutti / Sirelin Sillamaa / Emily Hoberg / Katarina A S Johansson / Urska Rovsnik / Sara Volta / ...Authors: Samantha Corrà / Alessandro Zuppardo / Sebastian Valenzuela / Louise Jenninger / Raffaele Cerutti / Sirelin Sillamaa / Emily Hoberg / Katarina A S Johansson / Urska Rovsnik / Sara Volta / Pedro Silva-Pinheiro / Hannah Davis / Aleksandra Trifunovic / Michal Minczuk / Claes M Gustafsson / Anu Suomalainen / Massimo Zeviani / Bertil Macao / Xuefeng Zhu / Maria Falkenberg / Carlo Viscomi /
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 ...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.
History
DepositionFeb 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase subunit gamma-1
B: DNA polymerase subunit gamma-2
C: DNA polymerase subunit gamma-2
P: DNA (primer strand)
T: DNA (template strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,9887
Polymers261,4805
Non-polymers5072
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA polymerase subunit gamma- ... , 2 types, 3 molecules ABC

#1: Protein DNA polymerase subunit gamma-1


Mass: 135078.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Polg / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q75WC0, DNA-directed DNA polymerase
#2: Protein DNA polymerase subunit gamma-2 / DNA polymerase gamma accessory 55 kDa subunit / p55 / Mitochondrial DNA polymerase accessory ...DNA polymerase gamma accessory 55 kDa subunit / p55 / Mitochondrial DNA polymerase accessory subunit / MtPolB / PolG-beta


Mass: 53229.684 Da / Num. of mol.: 2 / Mutation: A169T
Source method: isolated from a genetically manipulated source
Details: A169T (Single Nucleotide Polymorphism) / Source: (gene. exp.) Homo sapiens (human) / Gene: POLG2, MTPOLB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UHN1

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DNA chain , 2 types, 2 molecules PT

#3: DNA chain DNA (primer strand)


Mass: 7780.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (template strand)


Mass: 12162.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Chimeric mitochondrial DNA polymerase gamma ternary complex (mAhB) in replication conformerCOMPLEX#1-#40MULTIPLE SOURCES
2DNA polymerase subunit gamma-1ORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3DNA polymerase subunit gamma-2ORGANELLE OR CELLULAR COMPONENT#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
32Mus musculus (house mouse)10090
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
43Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 713960 / Symmetry type: POINT
RefinementHighest resolution: 2.54 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414566
ELECTRON MICROSCOPYf_angle_d0.48219903
ELECTRON MICROSCOPYf_dihedral_angle_d13.7195443
ELECTRON MICROSCOPYf_chiral_restr0.042129
ELECTRON MICROSCOPYf_plane_restr0.0042426

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