9OSO | pdb_00009oso

The specificity and structure of DNA crosslinking by a gut bacterial genotoxin

• PDB DOI: https://doi.org/10.2210/pdb9OSO/pdb
• NAKB: 9OSO
• BMRB: 31249

• Classification: DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-25 Released: 2025-11-19 
• Deposition Author(s): D'Souza, V.D., Balskus, E.P.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

The specificity and structure of DNA cross-linking by the gut bacterial genotoxin colibactin.

Carlson, E.S., Haslecker, R., Lecchi, C., Aguilar Ramos, M.A., Vennelakanti, V., Honaker, L., Stornetta, A., Millan, E.S., Johnson, B.A., Kulik, H.J., Balbo, S., Villalta, P.W., D'Souza, V.M., Balskus, E.P.

(2025) Science 390: eady3571-eady3571

• PubMed: 41343624 
• DOI: https://doi.org/10.1126/science.ady3571
• Primary Citation of Related Structures:  
  9OSO


• PubMed Abstract: 
  

  Accumulating evidence has connected the chemically unstable, DNA-damaging gut bacterial natural product colibactin to colorectal cancer, including the identification of mutational signatures that are thought to arise from colibactin-DNA interstrand cross-links (ICLs). However, we currently lack direct information regarding the structure of this lesion. In this work, we combined mass spectrometry and nuclear magnetic resonance spectroscopy to elucidate the specificity and structure of the colibactin-DNA ICL. We found that colibactin alkylates within the minor groove of adenine- and thymine-rich DNA, explaining the origins of mutational signatures. Unexpectedly, we discovered that the chemically unstable central motif of colibactin mediates the sequence specificity of cross-linking. By directly elucidating colibactin's interactions with DNA, this work enhances our understanding of the structure and genotoxic mechanisms of this cancer-linked gut bacterial natural product.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Structural Biology Initiative, City University of New York (CUNY) Advanced Science Research Center, New York, NY, USA.
Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 9.37 kDa 
• Atom Count: 624 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA-COLIBACTIN	A, B	14	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CEC (Subject of Investigation/LOI)	C [auth A]	N-({4-[(2R)-2-amino-2-{4-[(2-{(4Z)-2-methyl-4-[(5S)-5-methylpyrrolidin-2-ylidene]-5-oxo-4,5-dihydro-1H-pyrrol-3-yl}acetamido)acetyl]-1,3-thiazol-2-yl}acetyl]-1,3-thiazol-2-yl}methyl)-2-{(4Z)-2-methyl-4-[(5S)-5-methylpyrrolidin-2-ylidene]-5-oxo-4,5-dihydro-1H-pyrrol-3-yl}acetamide C35 H39 N9 O6 S2 VHOMKILVRMYTBO-ORFCZNMFSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): D'Souza, V.D., Balskus, E.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA208834
Howard Hughes Medical Institute (HHMI)	United States	55108516

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release
  
• Version 1.1: 2025-12-17
  Changes: Database references