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TitleOvercoming air-water interface-induced artifacts in Cryo-EM with protein nanocrates.
Journal, issue, pagesbioRxiv, Year 2025
Publish dateAug 18, 2025
AuthorsMatthew C Jenkins / Daija Bobe / Jake D Johnston / Jonah Cheung / Akira Karasawa / Christina M Zimanyi / Ömer Dermanci / M G Finn / Alex de Marco / Mykhailo Kopylov /
PubMed AbstractContact with the air-water interface can bias the orientation of macromolecules during cryo-EM sample preparation, leading to uneven sample distribution, preferred orientation, and damage to the ...Contact with the air-water interface can bias the orientation of macromolecules during cryo-EM sample preparation, leading to uneven sample distribution, preferred orientation, and damage to the molecules of interest. To prevent this, we describe a method to encapsulate target proteins within highly hydrophilic, structurally homogeneous, and stable protein shells, which we refer to as "nanocrates" for this purpose. Here, we describe packaging, data acquisition, and reconstruction of three proof-of-principle examples, each illuminating a different aspect of the method: apoferritin (ApoF, demonstrating high-resolution), thyroglobulin (Tg, solving a known preferred orientation problem), and 7,8-dihydroneopterin aldolase (DHNA, a structure previously uncharacterized by cryo-EM).
External linksbioRxiv / PubMed:40894667 / PubMed Central
MethodsEM (single particle)
Resolution1.74 - 1.75 Å
Structure data

72122

9q1b

EMDB-72122, PDB-9q1b:
MS2 bacteriophage coat protein after reassembly as a nanocrate (MS2nc) with no cargo and with waters modeled
Method: EM (single particle) / Resolution: 1.74 Å

72124

9q1d

EMDB-72124, PDB-9q1d:
MS2 bacteriophage coat protein with waters modeled
Method: EM (single particle) / Resolution: 1.75 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • escherichia phage ms2 (virus)
KeywordsVIRUS / Bacteriophage / VLP / MS2 / nanocrate

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