8FOE | pdb_00008foe

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

PDB DOI: https://doi.org/10.2210/pdb8FOE/pdb
EM Map EMD-29347: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2022-12-30 Released: 2023-05-31
Deposition Author(s): Yuan, Z., Georgescu, R., Li, H., O'Donnell, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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

PubMed: 37344454 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-39441-1
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 356.31 kDa
Atom Count: 15,747
Modeled Residue Count: 1,945
Deposited Residue Count: 3,110
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A [auth 1]	1,468	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: POL1 EC: 2.7.7.7
UniProt
Find proteins for P13382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P13382 Go to UniProtKB: P13382
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13382
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase	B [auth A]	409	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PRI1 EC: 2.7.7
UniProt
Find proteins for P10363 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10363 Go to UniProtKB: P10363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10363
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase large subunit	C [auth B]	528	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PRI2, GI527_G0003596
UniProt
Find proteins for P20457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20457 Go to UniProtKB: P20457
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20457
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase alpha subunit B	D [auth C]	705	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: POL12, GI527_G0000165
UniProt
Find proteins for P38121 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38121 Go to UniProtKB: P38121
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38121
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

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

Released Date: 2023-05-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM131754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115809
Howard Hughes Medical Institute (HHMI)	United States	M.E.O.