8V6J | pdb_00008v6j

DNA elongation complex (configuration 2) of Xenopus laevis DNA polymerase alpha-primase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8V6J

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 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.

Macromolecule Content 

  • Total Structure Weight: 328.23 kDa 
  • Atom Count: 19,600 
  • Modeled Residue Count: 2,344 
  • Deposited Residue Count: 2,734 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 1
  • Unique hybrid chains: 1

Macromolecules


Find similar proteins by:|  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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase alpha subunit B601Xenopus laevisMutation(s): 0 
Gene Names: pola2.L
UniProt
Find proteins for Q6DCZ1 (Xenopus laevis)
Explore Q6DCZ1 
Go to UniProtKB:  Q6DCZ1
Entity Groups
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UniProt GroupQ6DCZ1
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA primase423Xenopus laevisMutation(s): 0 
Gene Names: prim1.S
EC: 2.7.7
UniProt
Find proteins for Q800A4 (Xenopus laevis)
Explore Q800A4 
Go to UniProtKB:  Q800A4
Entity Groups
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UniProt GroupQ800A4
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Reference Sequence
Find similar nucleic acids by: 
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA template50synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 6
MoleculeChains LengthOrganismImage
RNA-DNA primer20synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGT

Query on DGT



Download:Ideal Coordinates CCD File
I [auth A]2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
K [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
L [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

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 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 StatesCA92584

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Database references