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- EMDB-27170: Human mitochondrial DNA polymerase gamma ternary complex with GT ... -

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Basic information

Entry
Database: EMDB / ID: EMD-27170
TitleHuman mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (local refinement of subunit A and primer/template DNA)
Map data
Sample
  • Complex: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer
KeywordsDNA-binding protein / DNA polymerase / TRANSFERASE-DNA complex / TRANSFERASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsPark J / Yin YW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI134611 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Polγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.
Authors: Joon Park / Geoffrey K Herrmann / Patrick G Mitchell / Michael B Sherman / Y Whitney Yin /
Abstract: Accurate replication of mitochondrial DNA (mtDNA) by DNA polymerase γ (Polγ) is essential for maintaining cellular energy supplies, metabolism, and cell cycle control. To illustrate the structural ...Accurate replication of mitochondrial DNA (mtDNA) by DNA polymerase γ (Polγ) is essential for maintaining cellular energy supplies, metabolism, and cell cycle control. To illustrate the structural mechanism for Polγ coordinating polymerase (pol) and exonuclease (exo) activities to ensure rapid and accurate DNA synthesis, we determined four cryo-EM structures of Polγ captured after accurate or erroneous incorporation to a resolution of 2.4-3.0 Å. The structures show that Polγ employs a dual-checkpoint mechanism to sense nucleotide misincorporation and initiate proofreading. The transition from replication to error editing is accompanied by increased dynamics in both DNA and enzyme, in which the polymerase relaxes its processivity and the primer-template DNA unwinds, rotates, and backtracks to shuttle the mismatch-containing primer terminus 32 Å to the exo site for editing. Our structural and functional studies also provide a foundation for analyses of Polγ mutation-induced human diseases and aging.
History
DepositionJun 1, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27170.png

Downloads & links

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Map

FileDownload / File: emd_27170.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum0.0 - 15.402839
Average (Standard dev.)0.43032455 (±0.7418251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27170_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Additional map: CryoSPARC unsharpened map from local refinement

Fileemd_27170_additional_1.map
AnnotationCryoSPARC unsharpened map from local refinement
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AxesZYX

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Half map: #2

Fileemd_27170_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_27170_half_map_2.map
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Sample components

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Entire : Human mitochondrial DNA polymerase gamma ternary complex with GT ...

EntireName: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer
Components
  • Complex: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer

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Supramolecule #1: Human mitochondrial DNA polymerase gamma ternary complex with GT ...

SupramoleculeName: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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: 7.2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CryoSPARC consensus map
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 1076466
FSC plot (resolution estimation)

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