9C52 | pdb_00009c52

Cryo-EM structure of the Strand displacement Complex (I) of Yeast Mitochondrial DNA polymerase Gamma (MIP1) with downstream DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Structural basis for intrinsic strand displacement activity of mitochondrial DNA polymerase.

Nayak, A.R.Sokolova, V.Sillamaa, S.Herbine, K.Sedman, J.Temiakov, D.

(2025) Nat Commun 16: 2417-2417

  • DOI: https://doi.org/10.1038/s41467-025-57594-z
  • Primary Citation of Related Structures:  
    9C51, 9C52, 9C53, 9D2I

  • PubMed Abstract: 

    Members of the Pol A family of DNA polymerases, found across all domains of life, utilize various strategies for DNA strand separation during replication. In higher eukaryotes, mitochondrial DNA polymerase γ relies on the replicative helicase TWINKLE, whereas the yeast ortholog, Mip1, can unwind DNA independently. Using Mip1 as a model, we present a series of high-resolution cryo-EM structures that capture the process of DNA strand displacement. Our data reveal previously unidentified structural elements that facilitate the unwinding of the downstream DNA duplex. Yeast cells harboring Mip1 variants defective in strand displacement exhibit impaired oxidative phosphorylation and loss of mtDNA, corroborating the structural observations. This study provides a molecular basis for the intrinsic strand displacement activity of Mip1 and illuminates the distinct unwinding mechanisms utilized by Pol A family DNA polymerases.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Thomas Jefferson University; 1020 Locust St, Philadelphia, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase gamma1,240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MIP1GI527_G0005701
EC: 2.7.7.7
UniProt
Find proteins for P15801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P15801
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15801
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Non-Template DNAB [auth N]23synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
Template DNAC [auth T]42synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
Primer DNAD [auth P]23synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTPHENIX1.21rc1_5127

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH GM131832

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references