8G9O

Complete DNA elongation subcomplex of Xenopus laevis DNA polymerase alpha-primase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase.

Mullins, E.A.Salay, L.E.Durie, C.L.Bradley, N.P.Jackman, J.E.Ohi, M.D.Chazin, W.J.Eichman, B.F.

(2024) Nat Struct Mol Biol 31: 777-790

  • DOI: https://doi.org/10.1038/s41594-024-01227-4
  • Primary Citation of Related Structures:  
    8G99, 8G9F, 8G9L, 8G9N, 8G9O, 8UCU, 8UCV, 8UCW, 8V5M, 8V5N, 8V5O, 8V6G, 8V6H, 8V6I, 8V6J

  • PubMed Abstract: 

    The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of Xenopus laevis polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5' end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer-template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase.


  • Organizational Affiliation

    Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit1,127Xenopus laevisMutation(s): 0 
Gene Names: pola1pola
EC: 2.7.7.7
UniProt
Find proteins for Q9DE46 (Xenopus laevis)
Explore Q9DE46 
Go to UniProtKB:  Q9DE46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9DE46
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunit513Xenopus laevisMutation(s): 0 
Gene Names: prim2.S
UniProt
Find proteins for A0A1L8G3G3 (Xenopus laevis)
Explore A0A1L8G3G3 
Go to UniProtKB:  A0A1L8G3G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L8G3G3
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by: 3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA template50synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA-DNA primer20synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM136401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118089
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesPO1CA92584

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-03-27
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Database references