8FOE

Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex bound to a template DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular choreography of primer synthesis by the eukaryotic Pol alpha-primase.

Yuan, Z.Georgescu, R.Li, H.O'Donnell, M.E.

(2023) Nat Commun 14: 3697-3697

  • DOI: https://doi.org/10.1038/s41467-023-39441-1
  • Primary Citation of Related Structures:  
    8FOC, 8FOD, 8FOE, 8FOH, 8FOJ, 8FOK

  • PubMed Abstract: 

    The eukaryotic polymerase α (Pol α) synthesizes an RNA-DNA hybrid primer of 20-30 nucleotides. Pol α is composed of Pol1, Pol12, Primase 1 (Pri1), and Pri2. Pol1 and Pri1 contain the DNA polymerase and RNA primase activities, respectively. It has been unclear how Pol α hands over an RNA primer from Pri1 to Pol1 for DNA primer extension, and how the primer length is defined. Here we report the cryo-EM analysis of yeast Pol α in the apo, primer initiation, primer elongation, RNA primer hand-off from Pri1 to Pol1, and DNA extension states, revealing a series of very large movements. We reveal a critical point at which Pol1-core moves to take over the 3'-end of the RNA from Pri1. DNA extension is limited by a spiral motion of Pol1-core. Since both Pri1 and Pol1-core are flexibly attached to a stable platform, primer growth produces stress that limits the primer length.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymeraseA [auth 1]1,468Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL1
UniProt
Find proteins for P13382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13382 
Go to UniProtKB:  P13382
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13382
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primaseB [auth A]409Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRI1
UniProt
Find proteins for P10363 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10363 
Go to UniProtKB:  P10363
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UniProt GroupP10363
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunitC [auth B]528Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PRI2GI527_G0003596
UniProt
Find proteins for P20457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P20457
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UniProt GroupP20457
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha subunit BD [auth C]705Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL12GI527_G0000165
UniProt
Find proteins for P38121 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38121 
Go to UniProtKB:  P38121
Entity Groups  
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UniProt GroupP38121
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
E [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 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 StatesGM131754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115809
Howard Hughes Medical Institute (HHMI)United StatesM.E.O.

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references