Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 268.72 kDa 
• Atom Count: 15,314 
• Modelled Residue Count: 1,832 
• Deposited Residue Count: 2,279 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

 8D37

Human mitochondrial DNA polymerase gamma ternary complex with GT basepair in replication conformer

• PDB DOI:  https://doi.org/10.2210/pdb8D37/pdb
• EM Map EMD-27155: EMDB EMDataResource

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2022-05-31 Released: 2023-05-24 
• Deposition Author(s): Park, J., Yin, Y.W.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.

Park, J., Herrmann, G.K., Mitchell, P.G., Sherman, M.B., Yin, Y.W.

(2023) Nat Struct Mol Biol 

• PubMed: 37202477 
• DOI: https://doi.org/10.1038/s41594-023-00980-2
• Primary Citation of Related Structures:  
  8D33, 8D37, 8D3R, 8D42


• PubMed 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 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.

---

Organizational Affiliation: 

Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase subunit gamma-1	A	1,245	Homo sapiens	Mutation(s): 0  Gene Names: POLG, MDP1, POLG1, POLGA EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for P54098 (Homo sapiens) Explore P54098  Go to UniProtKB:  P54098
PHAROS:  P54098

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase subunit gamma-2, mitochondrial	B, C	491	Homo sapiens	Mutation(s): 0  Gene Names: POLG2, MTPOLB
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHN1 (Homo sapiens) Explore Q9UHN1  Go to UniProtKB:  Q9UHN1
PHAROS:  Q9UHN1

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*TP*AP*C)-3')	D [auth P]	24	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	E [auth T]	28	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP (Subject of Investigation/LOI)	G [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
CA (Subject of Investigation/LOI)	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Park, J., Yin, Y.W.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI134611

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-05-31
  Changes: Database references