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1952: BAM Complex with Electron Density

Closed since about 5 years ago

Advanced Overall Prediction Electron Density

Summary

Created
February 04, 2021
Expires
Max points
100
Description

This protein is part of a large protein complex with multiple subunits, which was recently solved by cryo-electron microscopy (cryo-EM) at 4.2A resolution. Unfortunately, the solved structure could really use some work so we are hoping you can improve the structure. One end of the unfolded chain is close to its correct position in the electron density, but the rest of the chain is completely extended and will need to be refolded to fit in the density cloud. Keep in mind that this will not be easy, as 4.2A resolution results in a challenging electron density cloud to work with! The starting structure includes several locked protein fragments in the electron density cloud. These are additional proteins that are also present, and are expected to make interactions with the final folded structure. Good luck!

***More details about the native structure in the puzzle comments***

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Comments

BootsMcGraw Lv 1

The exploded version was not my highest scoring. My current score is completely and far away from the density cloud. No amount of manipulation inside the cloud will give me the score I had prior to moving it inside.

BootsMcGraw Lv 1

I was so taken aback at "locked" segments flying away that I undid the action and performed other actions, erasing the one that caused the explosion. I simply moved my protein inside the cloud and wiggled.

jeff101 Lv 1

<pre>I shared with scientists several solutions before and after segments 5-9 got ejected from the cloud. In each case, I was using ci=1 at low wiggle power and tried wiggle backbone. This gave a drastic change in the protein's shape, raised the score, and ejected segments 5-9 from the cloud.

Starting from the solution Je2b -91877.294,
wiggle backbone ejected segments 5-9 and
got to -10266.665 before I quit it. After
that, I did shake and then wiggle sidechains
to reach -7767.930. That's when I noticed
segments 5-9 had ejected. Then I used undo
to find which step did the actual ejection.

Starting from the solution Je2b -91842.788,
wiggle backbone ejected segments 5-9 and
got to -7087.026 before I quit it. Then I
used undo to restore -91842.788 and tried
wiggle backbone again. This time it ejected
segments 5-9 and got to -7086.563 before I
quit it.</pre></code>

beta_helix Staff Lv 1

We believe that we have found what caused this.

We plan to repost this same protein again soon, this time starting from the PDB model (so that you can hopefully improve on it :-)

Thanks again and our apologies for the trouble.