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1964: Unsolved Huge Cryo-EM Density: Beet Virus

Closed since almost 5 years ago

Overall Electron Density

Summary

Created
March 04, 2021
Expires
Max points
100
Description

We are very excited about this puzzle, because our collaborators who provided us with the 4 structures from Foldit's 2019 cryo-EM paper have been unable to solve this cryo-EM structure.
This will not be easy, because the full density has 46 symmetric monomers and we can't cut out a single copy of density for you (since we don't know the structure). Instead, we've sliced off a quarter of the entire density, which our collaborators estimate should be ~10 monomers. So keep this in mind, as we are only providing you with a single monomeric chain to fold. More details and pictures in the puzzle comments!

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Comments

Susume Lv 1

The cloud appears complete on the inner and outer donut surfaces, and you've told us it has been sliced through the donut to make a wedge. What about the other two planes, the ones parallel to the plate if you set the donut on a plate? Are they sliced through density that extends further in that direction, or is our cloud as tall as the donut gets?

beta_helix Staff Lv 1

Based on the image above, it definitely seems like the density has been sliced across the top and underneath it as well. I can ask the experimentalists if you like.

Bruno Kestemont Lv 1

Thanks for your comments but I'm still in the cloud. In the top image (similar with the ED we received), it's like a repetition 3.5 x the same cloud. Should we try to fit the protein into one of them (say in the middle)?

If it's th case, have we a tool to slice the density map in order to only keep what we want to use ?

horowsah Staff Lv 1

This may or may not address some of the issues with the large amount of density, but if you haven't tried using the radius slider yet, I think it helps for this sort of challenge.

APPAAP Lv 1

I think that the Cryo-EM Density given is the 1/8th of the whole nucleocapsid of the plant virus. Clearly there is the inside and outside of the cross section donut shape shown above. There are also 4 cut planes say the TOP, BOTTOM, LEFT and RIGHT, and I think that the the TOP or BOTTOM planes is somewhere in the middle of the nucleocapsid as shown in the whole donut cross section the other one TOP or BOTTOM is indeed the TOP or BOTTOM of Cryo-EM density of the nucleocapsid. Do you agree or I am missing something?