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TitleCryo-EM reveals ArnA contamination during purification of a ciliary protein complex.
Journal, issue, pagesActa Crystallogr D Struct Biol, Vol. 82, Issue Pt 5, Page 404-410, Year 2026
Publish dateMay 1, 2026
AuthorsXuguang Jiang / Masahide Kikkawa /
PubMed AbstractEndogenous Escherichia coli proteins can co-purify with recombinant targets and dominate cryo-EM datasets, yet often escape detection during standard biochemical quality control. In parallel to the ...Endogenous Escherichia coli proteins can co-purify with recombinant targets and dominate cryo-EM datasets, yet often escape detection during standard biochemical quality control. In parallel to the recent report by Caliseki and coworkers [Caliseki et al. (2025), Acta Cryst. D81, 545-557], we independently identified ArnA contamination while purifying a soluble, low-yield KIF17-IFT70 complex, ultimately obtaining a 3.23 Å resolution cryo-EM structure of ArnA rather than the intended target. Our results reinforce that ArnA enrichment reflects general features of His-tag affinity purification and can become particularly problematic in cryo-EM workflows when the intended target is low in yield or conformationally heterogeneous. By comparing biochemical behavior and cryo-EM outcomes, we outline why ArnA may evade SDS-PAGE and size-exclusion chromatography, and be underappreciated in routine mass spectrometry-based quality control, yet becomes structurally dominant in cryo-EM. These findings broaden the scope of the original study and highlight the need for early cryo-EM screening and improved contaminant awareness in structural biology.
External linksActa Crystallogr D Struct Biol / PubMed:41984507 / PubMed Central
MethodsEM (single particle)
Resolution3.23 Å
Structure data

67448

21ak

EMDB-67448, PDB-21ak:
Cryo-EM structure of the E. coli ArnA hexamer
Method: EM (single particle) / Resolution: 3.23 Å

Source
  • escherichia coli (E. coli)
KeywordsTRANSFERASE / Bifunctional enzyme / polymyxin resistance protein / antimicrobial resistance protein

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