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1045: VipB Cryo-EM Density: Ghost Density

Closed since about 11 years ago

Intermediate Overall Prediction Electron Density

Summary

Created
January 29, 2015
Expires
Max points
100
Description

This electron density puzzle is a little different from previous puzzles. We've provided you with a small EM density map, but only as a guide—fitting to the density will not affect your score! We want to see how well Foldit players can fold a protein with only the visual guidance of an electron density map. This is a small domain of the VipB protein, which is a component of the type VI secretion system in V. cholerae. After this puzzle closes, it may be reposted with normal density scoring.

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Comments

retiredmichael Lv 1

without the density score the scripts are distorting the shape, for example the scorpion tail is getting pulled into the rest of the fold.

Bautho Lv 1

The chain you can see in the electron density is longer than the given chain of amino acids. If you directly start to fit one end of the chain into the density, the residues won't fit properly.
It looks like that there are about 5-6 residues missing after residue 114 (C-terminus) and about 4 residues missing before the first residue (N-terminus).

Bletchley Park Lv 1

There is also something odd about residu 114. It cannot be changed. It will remain a loop. Residu 1 does not have this limitation. Is this intentional or an artifact ?

gitwut Lv 1

Sorry, but I really dislike ED puzzles, and this one is no exception. There is always too much clutter. If it were possible to toggle sidechains on/off on the cloud it would probably be easier. This cloud is better than most of the previous EDs, but I might do as well or better working it as a denovo.

I know that seeing the sidechains can occasionally give extra clues, but when trying to determine the SS/backbone, they're more a hindrance than help.