8BTG

Cryo-EM structure of the bacterial replication origin opening basal unwinding system


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The bacterial replication origin BUS promotes nucleobase capture.

Pelliciari, S.Bodet-Lefevre, S.Fenyk, S.Stevens, D.Winterhalter, C.Schramm, F.D.Pintar, S.Burnham, D.R.Merces, G.Richardson, T.T.Tashiro, Y.Hubbard, J.Yardimci, H.Ilangovan, A.Murray, H.

(2023) Nat Commun 14: 8339

  • DOI: https://doi.org/10.1038/s41467-023-43823-w
  • Primary Citation of Related Structures:  
    8BTG, 8BV3

  • PubMed Abstract: 

    Genome duplication is essential for the proliferation of cellular life and this process is generally initiated by dedicated replication proteins at chromosome origins. In bacteria, DNA replication is initiated by the ubiquitous DnaA protein, which assembles into an oligomeric complex at the chromosome origin (oriC) that engages both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) to promote DNA duplex opening. However, the mechanism of DnaA specifically opening a replication origin was unknown. Here we show that Bacillus subtilis DnaA ATP assembles into a continuous oligomer at the site of DNA melting, extending from a dsDNA anchor to engage a single DNA strand. Within this complex, two nucleobases of each ssDNA binding motif (DnaA-trio) are captured within a dinucleotide binding pocket created by adjacent DnaA proteins. These results provide a molecular basis for DnaA specifically engaging the conserved sequence elements within the bacterial chromosome origin basal unwinding system (BUS).


  • Organizational Affiliation

    Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosomal replication initiator protein DnaA
A, B, C, D, E
A, B, C, D, E, F, G
446Bacillus subtilisMutation(s): 0 
Gene Names: dnaAB4417_2456C0W65_09430CFD21_00040J5227_06470NRS6116_00005NRS6202_21170SC09_Contig28orf00336
UniProt
Find proteins for A0A063XAK9 (Bacillus subtilis)
Explore A0A063XAK9 
Go to UniProtKB:  A0A063XAK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A063XAK9
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*CP*TP*TP*AP*TP*CP*CP*AP*CP*AP*AP*AP*TP*CP*CP*AP*CP*AP*GP*GP*CP*CP*C)-3')H [auth X]24DNA molecule
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (41-MER)I [auth Y]41DNA molecule
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
K [auth A]
M [auth B]
O [auth C]
Q [auth D]
S [auth E]
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
W [auth G]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth E],
V [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom204985/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release