Unknown particles in sample

3D Classification
1

Hi Everyone,

I’m not sure if this is the right place to post this, but I’m hoping someone maybe has an answer or can point me in the right direction.

Our NSEM lab does lots of EMPEM with HIV-1 Env and antibodies/Fabs. We occasionally see these particles in the micrographs and in the 2D classifications for these samples. We seem to only observe them in these EMPEM samples that have been run through an FPLC. We recently encountered one sample that had tons of these mystery particles - enough that we could get a decent 3D reconstruction out of them.

Has anyone seen anything like this before?

Screenshot 2024-02-29 at 11.19.11 AM
Screenshot 2024-02-29 at 11.19.11 AM1091×1092 301 KB

2

Screenshot 2024-02-29 at 11.56.54 AM
Screenshot 2024-02-29 at 11.56.54 AM813×330 22.5 KB

3

Screenshot 2024-02-29 at 11.58.46 AM
Screenshot 2024-02-29 at 11.58.46 AM1800×526 119 KB

4

What are the dimensions? D2 symmetry? What cells are the components generated in? I would guess an oligomeric enzyme of some sort but not sure exactly which…

2 Likes
5

Dimensions of the 2D classification box are 384Å, so the particle is roughly 190Å long and 100Å wide. C1 symmetry. Not sure what cells the components are generated in, they are made in another lab

1 Like
6

C1 symmetry, really? Looks dihedral? Or do you just mean you haven’t enforced symmetry during refinement/reconstruction?

2 Likes
7

I meant that symmetry wasn’t enforced! Sorry for the confusion

1 Like
8

You can run “omokage” search for shape and size similarity among other volumes. Shape similarity search of macromolecules - Omokage search

2 Likes
9

100% positive this is alpha-2-macroglobulin.

See 2D/volumes from:

4 Likes
10

That’s definitely it! Thank you so much!