8FAK | pdb_00008fak

DNA replication fork binding triggers structural changes in the PriA DNA helicase that regulate the PriA-PriB replication restart pathway in E. coli

• PDB DOI: https://doi.org/10.2210/pdb8FAK/pdb
• EM Map EMD-28959: EMDB EMDataResource
• NAKB: 8FAK

• Classification: HELICASE/DNA
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-28 Released: 2023-05-10 
• Deposition Author(s): Duckworth, A.T., Ducos, P.L., McMillan, S.D., Satyshur, K.A., Blumenthal, K.H., Deorio, H.R., Larson, J.A., Sandler, S.J., Grant, T., Keck, J.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Replication fork binding triggers structural changes in the PriA helicase that govern DNA replication restart in E. coli.

Duckworth, A.T., Ducos, P.L., McMillan, S.D., Satyshur, K.A., Blumenthal, K.H., Deorio, H.R., Larson, J.A., Sandler, S.J., Grant, T., Keck, J.L.

(2023) Nat Commun 14: 2725-2725

• PubMed: 37169801 
• DOI: https://doi.org/10.1038/s41467-023-38144-x
• Primary Citation Related Structures: 
  8FAK


• PubMed Abstract: 
  

  Bacterial replisomes often dissociate from replication forks before chromosomal replication is complete. To avoid the lethal consequences of such situations, bacteria have evolved replication restart pathways that reload replisomes onto prematurely terminated replication forks. To understand how the primary replication restart pathway in E. coli (PriA-PriB) selectively acts on replication forks, we determined the cryogenic-electron microscopy structure of a PriA/PriB/replication fork complex. Replication fork specificity arises from extensive PriA interactions with each arm of the branched DNA. These interactions reshape the PriA protein to create a pore encircling single-stranded lagging-strand DNA while also exposing a surface of PriA onto which PriB docks. Together with supporting biochemical and genetic studies, the structure reveals a switch-like mechanism for replication restart initiation in which restructuring of PriA directly couples replication fork recognition to PriA/PriB complex formation to ensure robust and high-fidelity replication re-initiation.

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Organizational Affiliation: 
• Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, USA.
Department of Microbiology, University of Massachusetts at Amherst, Amherst, MA, 01003, USA. [e-mail].
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA. [e-mail].
John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, USA. [e-mail].
Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 133.99 kDa 
• Atom Count: 7,715 
• Modeled Residue Count: 894 
• Deposited Residue Count: 1,035 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Primosomal replication protein N	A, B	104	Escherichia coli K-12	Mutation(s): 0  Gene Names: priB, b4201, JW4159
UniProt
Find proteins for P07013 (Escherichia coli (strain K12)) Explore P07013  Go to UniProtKB:  P07013

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Primosomal protein N'	D [auth H]	732	Escherichia coli K-12	Mutation(s): 0  Gene Names: priA, b3935, JW3906 EC: 3.6.4 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for P17888 (Escherichia coli (strain K12)) Explore P17888  Go to UniProtKB:  P17888

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*GP*AP*CP*TP*CP*AP*TP*TP*TP*AP*GP*CP*CP*CP*TP*TP*AP*TP*CP*CP*G)-3')	C [auth G]	40	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*AP*TP*AP*AP*GP*GP*GP*CP*TP*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*A)-3')	E [auth J]	40	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')	F [auth Z]	15	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth H], H	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cisTEM	2.0.0
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Duckworth, A.T., Ducos, P.L., McMillan, S.D., Satyshur, K.A., Blumenthal, K.H., Deorio, H.R., Larson, J.A., Sandler, S.J., Grant, T., Keck, J.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM098885

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-05-24
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary