9ZBT | pdb_00009zbt

Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome

• PDB DOI: https://doi.org/10.2210/pdb9ZBT/pdb
• EM Map EMD-74008: EMDB EMDataResource

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


• Deposited: 2025-11-21 Released: 2026-05-27 
• Deposition Author(s): Duckworth, A.T., Keck, J.L., Grant, T.
• 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

Visualization of the complete preprimosome reveals the structural mechanisms governing DNA replication restart.

Ducos, P.L., Duckworth, A.T., Satyshur, K.A., Keck, J.L., Grant, T.

(2026) Nat Commun 

• PubMed: 42140935 
• DOI: https://doi.org/10.1038/s41467-026-73239-1
• Primary Citation Related Structures: 
  9ZBT, 9ZBU


• PubMed Abstract: 
  

  Replication restart pathways reinitiate DNA replication processes following their premature termination. In Escherichia coli, this essential process begins with regulated assembly of the preprimosome complex, comprising the PriA, PriB, and DnaT proteins, onto an abandoned replication fork. Here, we present two distinct preprimosome structures. One represents an intermediate stage in preprimosome assembly with a single DnaT C-terminal domain (DnaT ^CTD ) bound to PriA/PriB/DNA. The second captures the mature preprimosome, in which filamentation of multiple DnaT ^CTD molecules catalyzes the handoff of the single-stranded lagging-strand DNA from PriB to DnaT. The DnaT N-terminal domain forms a separate, independent oligomer in the mature structure. Taken together, our results detail the molecular mechanisms underlying replication restart initiation and regulation and suggest mechanistic similarities between DnaT and the canonical initiator protein DnaA.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 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: 153.46 kDa 
• Atom Count: 9,594 
• Modeled Residue Count: 1,098 
• Deposited Residue Count: 1,214 
• Unique protein chains: 3
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication restart protein DnaT	A [auth D]	179	Escherichia coli K-12	Mutation(s): 0  Gene Names: dnaT, b4362, JW4326
UniProt
Find proteins for P0A8J2 (Escherichia coli (strain K12)) Explore P0A8J2  Go to UniProtKB:  P0A8J2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication restart protein PriB	B [auth A], C [auth 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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Primosomal protein N'	E [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: 3
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	D [auth G]	40	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	F [auth J]	40	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (11-MER)	G [auth Z]	15	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	H, I [auth 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
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Duckworth, A.T., Keck, J.L., Grant, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	RO1GM098885

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release