6V93

Structure of DNA Polymerase Zeta/DNA/dNTP Ternary Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and mechanism of B-family DNA polymerase zeta specialized for translesion DNA synthesis.

Malik, R.Kopylov, M.Gomez-Llorente, Y.Jain, R.Johnson, R.E.Prakash, L.Prakash, S.Ubarretxena-Belandia, I.Aggarwal, A.K.

(2020) Nat Struct Mol Biol 27: 913-924

  • DOI: https://doi.org/10.1038/s41594-020-0476-7
  • Primary Citation of Related Structures:  
    6V8P, 6V93

  • PubMed Abstract: 

    DNA polymerase ζ (Polζ) belongs to the same B-family as high-fidelity replicative polymerases, yet is specialized for the extension reaction in translesion DNA synthesis (TLS). Despite its importance in TLS, the structure of Polζ is unknown. We present cryo-EM structures of the Saccharomyces cerevisiae Polζ holoenzyme in the act of DNA synthesis (3.1 Å) and without DNA (4.1 Å). Polζ displays a pentameric ring-like architecture, with catalytic Rev3, accessory Pol31' Pol32 and two Rev7 subunits forming an uninterrupted daisy chain of protein-protein interactions. We also uncover the features that impose high fidelity during the nucleotide-incorporation step and those that accommodate mismatches and lesions during the extension reaction. Collectively, we decrypt the molecular underpinnings of Polζ's role in TLS and provide a framework for new cancer therapeutics.


  • Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase zeta catalytic subunit1,538Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: REV3PSO1YPL167CP2535
EC: 2.7.7.7
UniProt
Find proteins for P14284 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P14284
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase zeta processivity subunitB [auth D],
C [auth E]
245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: REV7YIL139C
UniProt
Find proteins for P38927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38927
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta small subunitD [auth F]494Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: POL31HUS2HYS2SDP5YJR006WJ1427YJR83.7
EC: 2.7.7.7
UniProt
Find proteins for P46957 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46957
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta subunit 3E [auth G]350Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: POL32YJR043CJ1626
UniProt
Find proteins for P47110 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47110
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNAF [auth P],
G [auth T]
30synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesR01-GM124047

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references