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Yorodumi- EMDB-27170: Human mitochondrial DNA polymerase gamma ternary complex with GT ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27170 | |||||||||
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Title | Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer (local refinement of subunit A and primer/template DNA) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA-binding protein / DNA polymerase / TRANSFERASE-DNA complex / TRANSFERASE | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||
Authors | Park J / Yin YW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27170.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-27170-v30.xml emd-27170.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27170_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_27170.png | 141.7 KB | ||
Masks | emd_27170_msk_1.map | 125 MB | Mask map | |
Others | emd_27170_additional_1.map.gz emd_27170_half_map_1.map.gz emd_27170_half_map_2.map.gz | 62.7 MB 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27170 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27170 | HTTPS FTP |
-Validation report
Summary document | emd_27170_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_27170_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_27170_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_27170_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27170 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27170 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27170.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27170_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: CryoSPARC unsharpened map from local refinement
File | emd_27170_additional_1.map | ||||||||||||
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Annotation | CryoSPARC unsharpened map from local refinement | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_27170_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27170_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human mitochondrial DNA polymerase gamma ternary complex with GT ...
Entire | Name: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer |
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Components |
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-Supramolecule #1: Human mitochondrial DNA polymerase gamma ternary complex with GT ...
Supramolecule | Name: Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in editing conformer type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |