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2415: Electron Density Reconstruction 77

Closed since about 2 years ago

Novice Overall Prediction Electron Density

Summary

Created
February 01, 2024
Expires
Max points
100
Description

The structure of this protein has already been solved and published, but close inspection suggests that there are some problems with the published solution. We'd like to see if Foldit players can use the same electron density data to reconstruct a better model. It's a monomer, but not every segment may be visible. Also, if you're wondering if this is an example of a complete, well-folded globular protein like we tend to encourage Foldit players to go for, it's not. It's a part of a fibrous structural protein, and so on its own it might look a bit funny, but it's still helpful for understanding the function of the protein to improve the modeling.

Sequence
LAAKEAKLRDLEDSLARERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGEEER

Top groups

  1. Avatar for AlphaFold 11. AlphaFold 1 pt. 15,260
  2. Avatar for Beta Folders 12. Beta Folders 1 pt. 14,124
  1. Avatar for roarshock 31. roarshock Lv 1 4 pts. 15,744
  2. Avatar for SemperRabbit 32. SemperRabbit Lv 1 3 pts. 15,733
  3. Avatar for rosie4loop 33. rosie4loop Lv 1 3 pts. 15,712
  4. Avatar for manu8170 34. manu8170 Lv 1 2 pts. 15,670
  5. Avatar for kitsoune 35. kitsoune Lv 1 2 pts. 15,666
  6. Avatar for pizpot 36. pizpot Lv 1 2 pts. 15,660
  7. Avatar for zbp 37. zbp Lv 1 2 pts. 15,635
  8. Avatar for Vinara 38. Vinara Lv 1 1 pt. 15,626
  9. Avatar for ShadowTactics 39. ShadowTactics Lv 1 1 pt. 15,597
  10. Avatar for Oransche 40. Oransche Lv 1 1 pt. 15,558

Comments

horowsah Staff Lv 1

Some of the reconstruction puzzles are on very similar proteins, sometimes on proteins that are the same but one is mutated for various reasons, and sometimes even the same protein. There are certain proteins that are thought of as "test" proteins for crystallography methods, and so they and variants of them are over-represented in the PDB. That said, some of those structures are still in need of major improvement. One might think that's silly, since it seems that the authors could have used the older structures as guides. In some cases, that's a perfectly valid criticism, but in other cases they specifically want to blind themselves to test their new methods, and sometimes that doesn't turn out so well. These days, the PDB wouldn't be happy about having such structures deposited, since it will muck up the structure quality of the PDB for others to use, but it used to be perfectly fine, and it's still possible to do it even today.