[3dem] A strong density in the cryo-EM map

[Dr. Alexander Belyy]

Dear community of structural biologists,

In a 3.5 Å cryo-EM reconstruction, we have discovered a large density of 10-12 Å diameter that we are having difficulty identifying (see attachment). This density is surrounded by 5 arginines, 3 asparagines, 2 glutamines, 1 aspartate, and 1 glutamate coming from 4 different regions of the protein. Functionally, the density is needed to hold the protein together. This density appears at higher thresholds than the protein itself and is visible even at the 2D class level. After local refinement and sharpening, the density becomes pyramid-like with a series of smaller spheres with pseudosymmetry (or C3?).

We would be grateful for any suggestions as to what this might be.

Thank you!

Best regards from Dortmund,
Alexander
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