3DVA for crosslinked disordered domains of a protein

I am currently solving several complexes each of which have a completely disordered domain. So much so that the domain has only shown up so far when I fix the complex with 0.1% glutaraldehyde. I have also solved the non-crosslinked version of the same complex, and it goes to higher resolution but this domain completely disappears from the map. This disordered domain is heavily glycosylated has also otherwise been refractory to structural studies in general. 3DVA itself is a very impressive tool, so this could be more of a hypothetical question but - would 3DVA work on a case like this? I am trying it anyway but curious if anyone has their experience to share.


HI @aparvate it would be great to hear what you found in this case!
However my guess is that 3DVA won’t be able to resolve the dissapearing domain. The reason is that if the domain is truly “disordered”, it will have many many degrees of freedom in its flexibility. 3DVA (and all heterogeneity methods in fact) are limited to being able to resolve only a small number of degrees of freedom. So when there is rotational motion, or bending, or twisting etc, a few degrees of freedom can describe that flexibility. But full disorder (where the domain does not have much conserved structural similarity from one image to another) is out of the realm of possibility right now for single particle cryo-EM.

Hey Ali
Thanks for the reply!