21AK

Cryo-EM structure of the E. coli ArnA hexamer

Summary for 21AK

• Entry DOI: 10.2210/pdb21ak/pdb
• EMDB information: 67448
• Descriptor: Bifunctional polymyxin resistance protein ArnA (1 entity in total)
• Functional Keywords: bifunctional enzyme, polymyxin resistance protein, antimicrobial resistance protein, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 12
• Total formula weight: 892629.28

Authors

Jiang, X.,Kikkawa, M. (deposition date: 2025-12-04, release date: 2026-03-25, Last modification date: 2026-05-13)

Primary citation

Jiang, X.,Kikkawa, M.
Cryo-EM reveals ArnA contamination during purification of a ciliary protein complex.
Acta Crystallogr D Struct Biol, 82:404-410, 2026

PubMed Abstract: 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.

PubMed: 41984507
DOI: 10.1107/S2059798326002846

Experimental method

ELECTRON MICROSCOPY (3.23 Å)