8V5R | pdb_00008v5r

Active conformation of DNA polymerase gamma bound to DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8V5R

This is version 1.2 of the entry. See complete history

Literature

Coordinated DNA polymerization by Pol gamma and the region of LonP1 regulated proteolysis.

Riccio, A.A.Brannon, A.J.Krahn, J.M.Bouvette, J.Williams, J.G.Borgnia, M.J.Copeland, W.C.

(2024) Nucleic Acids Res 52: 7863-7875

  • DOI: https://doi.org/10.1093/nar/gkae539
  • Primary Citation Related Structures: 
    8V54, 8V55, 8V5D, 8V5R

  • PubMed Abstract: 

    The replicative mitochondrial DNA polymerase, Polγ, and its protein regulation are essential for the integrity of the mitochondrial genome. The intricacies of Polγ regulation and its interactions with regulatory proteins, which are essential for fine-tuning polymerase function, remain poorly understood. Misregulation of the Polγ heterotrimer, consisting of (i) PolG, the polymerase catalytic subunit and (ii) PolG2, the accessory subunit, ultimately results in mitochondrial diseases. Here, we used single particle cryo-electron microscopy to resolve the structure of PolG in its apoprotein state and we captured Polγ at three intermediates within the catalytic cycle: DNA bound, engaged, and an active polymerization state. Chemical crosslinking mass spectrometry, and site-directed mutagenesis uncovered the region of LonP1 engagement of PolG, which promoted proteolysis and regulation of PolG protein levels. PolG2 clinical variants, which disrupted a stable Polγ complex, led to enhanced LonP1-mediated PolG degradation. Overall, this insight into Polγ aids in an understanding of mitochondrial DNA replication and characterizes how machinery of the replication fork may be targeted for proteolytic degradation when improperly functioning.


  • Organizational Affiliation
    • Mitochondrial DNA Replication group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.

Macromolecule Content 

  • Total Structure Weight: 287.05 kDa 
  • Atom Count: 15,338 
  • Modeled Residue Count: 1,785 
  • Deposited Residue Count: 2,308 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-11,229Homo sapiensMutation(s): 2 
Gene Names: POLG
EC: 2.7.7.7 (UniProt), 3.1.11 (UniProt), 4.2.99 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P54098 (Homo sapiens)
Explore P54098 
Go to UniProtKB:  P54098
PHAROS:  P54098
GTEx:  ENSG00000140521 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54098
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase subunit gamma-2, mitochondrial
B, C
474Homo sapiensMutation(s): 0 
Gene Names: POLG2MTPOLB
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHN1 (Homo sapiens)
Explore Q9UHN1 
Go to UniProtKB:  Q9UHN1
PHAROS:  Q9UHN1
GTEx:  ENSG00000256525 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHN1
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
primer DNAD [auth P]51Homo sapiens
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
Template DNAE [auth T]80Homo sapiens
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D3T

Query on D3T



Download:Ideal Coordinates CCD File
G [auth A]2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01 ES065078
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01 ES065080

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-14
    Changes: Data collection, Structure summary