Placeholder image of a protein
Icon representing a puzzle

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.

Top groups

  1. Avatar for Deleted group 21. Deleted group pts. 7,236
  2. Avatar for StructuralBiology-CHEM490 22. StructuralBiology-CHEM490 1 pt. 7,165
  3. Avatar for Russian team 23. Russian team 1 pt. 6,906
  4. Avatar for Deleted group 24. Deleted group pts. 6,762
  5. Avatar for Deleted group 25. Deleted group pts. 6,543
  6. Avatar for It's over 9000! 26. It's over 9000! 1 pt. 6,500
  7. Avatar for Eὕρηκα! Heureka! 27. Eὕρηκα! Heureka! 1 pt. 5,634
  8. Avatar for Team South Africa 28. Team South Africa 1 pt. 5,622
  9. Avatar for Crunching Family 29. Crunching Family 1 pt. 4,927
  10. Avatar for Cell Biology Spring 2015 with Smith 30. Cell Biology Spring 2015 with Smith 1 pt. 4,565
  1. Avatar for basakd 221. basakd Lv 1 1 pt. 3,768
  2. Avatar for EffJay 222. EffJay Lv 1 1 pt. 3,684
  3. Avatar for guineapig 223. guineapig Lv 1 1 pt. 3,573
  4. Avatar for MadTrumpeter 224. MadTrumpeter Lv 1 1 pt. 3,554
  5. Avatar for KarenCH 225. KarenCH Lv 1 1 pt. 3,386
  6. Avatar for sushi810 226. sushi810 Lv 1 1 pt. 3,206
  7. Avatar for bataebi 227. bataebi Lv 1 1 pt. 3,111
  8. Avatar for jermainiac 228. jermainiac Lv 1 1 pt. 3,111
  9. Avatar for MJIlgenfritz 229. MJIlgenfritz Lv 1 1 pt. 3,070
  10. Avatar for grogar7 230. grogar7 Lv 1 1 pt. 2,955

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.