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- EMDB-51113: Mouse mitochondrial DNA polymerase gamma ternary complex in error... -

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Basic information

Entry
Database: EMDB / ID: EMD-51113
TitleMouse mitochondrial DNA polymerase gamma ternary complex in error-editing conformer (local refinement of subunit B)
Map datalocal refinement map of subunit B
Sample
  • Complex: Mouse mitochondrial DNA polymerase gamma ternary complex in error-editing conformer
    • Organelle or cellular component: DNA polymerase subunit gamma-1
    • Organelle or cellular component: DNA polymerase subunit gamma-2
KeywordsMitochondrial DNA polymerase / TRANSFERASE
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsValenzuela S / Falkenberg M
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Other private 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
DepositionJul 19, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51113.png

Downloads & links

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Map

FileDownload / File: emd_51113.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement map of subunit B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-36.912415000000003 - 60.892932999999999
Average (Standard dev.)0.00064317306 (±0.98599267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51113_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancermap

Fileemd_51113_additional_1.map
AnnotationDeepEMhancermap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_51113_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoSPARC half-map A

Fileemd_51113_half_map_1.map
AnnotationcryoSPARC half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoSPARC half-map B

Fileemd_51113_half_map_2.map
AnnotationcryoSPARC half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse mitochondrial DNA polymerase gamma ternary complex in error...

EntireName: Mouse mitochondrial DNA polymerase gamma ternary complex in error-editing conformer
Components
  • Complex: Mouse mitochondrial DNA polymerase gamma ternary complex in error-editing conformer
    • Organelle or cellular component: DNA polymerase subunit gamma-1
    • Organelle or cellular component: DNA polymerase subunit gamma-2

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Supramolecule #1: Mouse mitochondrial DNA polymerase gamma ternary complex in error...

SupramoleculeName: Mouse mitochondrial DNA polymerase gamma ternary complex in error-editing conformer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: DNA polymerase subunit gamma-1

SupramoleculeName: DNA polymerase subunit gamma-1 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: DNA polymerase subunit gamma-2

SupramoleculeName: DNA polymerase subunit gamma-2 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSPARC ab-initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 930574
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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