9P9A | pdb_00009p9a

DnaB complex binding with ssDNA and dTDP-AlFx


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9P9A

This is version 1.2 of the entry. See complete history

Literature

Cellular replisomes are powered by flex-fuel motors for unwinding DNA.

Rashid, F.Pangeni, S.Liu, C.Kumar, H.Moon, G.S.Yan, Q.Ha, T.Berger, J.M.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-73652-6
  • Primary Citation Related Structures: 
    9P9A

  • PubMed Abstract: 

    DNA replication relies on hexameric, ring-shaped helicases to unwind parental DNA for supporting fork progression over tens of thousands of base pairs. Oddly, biochemical studies have suggested that, on their own, replicative helicases are rather limited motors that struggle to couple rapid movement to nucleotide turnover (typically believed to be solely ATP). Here, single-molecule studies reveal that when properly loaded, the Escherichia coli (E. coli) replicative helicase, DnaB, is a tremendously fast single-stranded DNA translocase that moves up to three times more rapidly than the replisome (3 knt/s). Translocation is highly processive, resistant to pulling force/high salt, and can displace short, 3'-tailed DNA duplexes without apparent changes in speed. Surprisingly, we find that the loader for DnaB, DnaC, can use any rNTP or dATP for depositing DnaB onto ssDNA and that the helicase itself also must hydrolyze nucleotide for stable loading. DnaB translocation also turns out to be supported by any r/dNTP, a property shown to extend to the eukaryotic CMG replicative helicase. Overall, the DNA unwinding engines that support cellular replisomes are highly indiscriminate of their fuel source, a feature that may be of utility during times when cells encounter nucleotide pool stress but have committed to DNA synthesis.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 310.75 kDa 
  • Atom Count: 12,968 
  • Modeled Residue Count: 1,613 
  • Deposited Residue Count: 2,737 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Replicative DNA helicase DnaB
A,
B,
C,
D,
E [auth H],
F
454Geobacillus stearothermophilusMutation(s): 0 
Gene Names: dnaB
EC: 5.6.2.3
UniProt
Find proteins for Q9X4C9 (Geobacillus stearothermophilus)
Explore Q9X4C9 
Go to UniProtKB:  Q9X4C9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X4C9
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')G [auth M]13synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYD
(Subject of Investigation/LOI)

Query on TYD



Download:Ideal Coordinates CCD File
I [auth A],
M [auth C],
O [auth D],
R [auth H],
U [auth F]
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
ALF

Query on ALF



Download:Ideal Coordinates CCD File
J [auth A],
K [auth B],
P [auth D],
S [auth H],
V [auth F]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
L [auth C],
N [auth D],
Q [auth H],
T [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-24
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Data collection, Database references
  • Version 1.2: 2026-07-22
    Changes: Data collection, Structure summary