9Q1B

MS2 bacteriophage coat protein after reassembly as a nanocrate (MS2nc) with no cargo and with waters modeled

Summary for 9Q1B

• Entry DOI: 10.2210/pdb9q1b/pdb
• EMDB information: 72122
• Descriptor: Capsid protein (2 entities in total)
• Functional Keywords: bacteriophage, vlp, ms2, nanocrate, virus
• Biological source: Escherichia phage MS2
• Total number of polymer chains: 3
• Total formula weight: 41215.39

Authors

Zimanyi, C.M.,Bobe, D.,Jenkins, M.C.,Kopylov, M. (deposition date: 2025-08-13, release date: 2025-08-27, Last modification date: 2026-09-16)

Primary citation

Jenkins, M.C.,Bobe, D.,Johnston, J.D.,Cheung, J.,Karasawa, A.,Zimanyi, C.M.,Dermanci, O.,McManus, C.T.,Finn, M.G.,de Marco, A.,Kopylov, M.
Overcoming air-water interface-induced artifacts in cryo-EM with protein nanocrates.
Nat.Methods, 23:1798-1804, 2026

PubMed Abstract: Contact with the air-water interface can bias the orientation of macromolecules during cryo-electron microscopy 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 the packaging, data acquisition and reconstruction of three proof-of-principle examples, each illuminating a different aspect of the method: apoferritin (demonstrating high-resolution), thyroglobulin (solving a known preferred orientation problem) and 7,8-dihydroneopterin aldolase (a structure previously uncharacterized by cryo-electron microscopy).

PubMed: 42637978
DOI: 10.1038/s41592-026-03184-w

Experimental method

ELECTRON MICROSCOPY (1.74 Å)