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2705: Electron Density Reconstruction 150

Closed since 2 months ago

Novice Overall Prediction Electron Density

Summary

Created
December 17, 2025
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. This puzzle has two identical chains, and comes from PDB entry 2GFP. It's large, so the trim tool is recommended.

Sequence
LLLMLVLLVAVGQMAQTIYIPAIADMARDLNVREGAVQSVMGAYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFMLATLVAVTTSSLTVLIAASAMQGMGTGVGGVMARTLPRDLYERTQLRHANSLLNMGILVSPLLAPLIGGLLDTMWNWRACYLFLLVLCAGVTFSMARWMPETRPVDAPRTRLLTSYKTLFGNSGFNCYLLMLIGGLAGIAAFEACSGVLMGAVLGLSSMTVSILFILPIPAAFFGAWFAGRPNKRFSTLMWQSVICCLLAGLLMWIPDWFGVMNVWTLLVPAALFFFGAGMLFPLATSGAMEPFPFLAGTAGALVGGLQNIGSGVLASLSAMLPQTGQGSLGLLMTLMGLLIVLCWLPL

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Comments

rmoretti Staff Lv 1

When experimentalists determine the density, they get the results for the "asymmetric unit" (the repeating unit which makes up the crystal structure). Sometimes this can contain more than one identical chain. Sometimes these repeated chains in the asymmetric unit are in the same structure, but sometimes there's significant structural differences between the two copies (which reflects itself in a difference in the density). As such, when you're figuring out the structure from the density, you have to treat the two halves of the density differently, modeling each with an independent chain.

If things are getting too large – to the point where it's inhibiting your ability to work on this (or any) puzzle, even when using trim – please let us know. There are possible work-arounds (like segmenting the density into two puzzles), but we're likely to get better scientific results by modeling both chains at once.