2663: Electron Density Reconstruction 136

Closed since 6 months ago

Summary

• Created: September 10, 2025
• Expires: September 25, 2025 at 18:00 UTC
• 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 four copies of the same small protein, but not all the segments that are visible are the same.

• Sequence: MVRANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTNKKRPAATERSEQIQMEF

Top groups

• 11. Gargleblasters 1 pt. 34,482
• 12. SETI.Germany 1 pt. 34,278
• 13. BOINC@Poland 1 pt. 33,640
• 14. Mahmut Oyunda 1 pt. 32,315
• 15. Russian team 1 pt. 32,310
• 16. BCH3025 S25 1 pt. 27,936

Top soloists

• 1. spvincent 100 pts. 37,400
• 2. LociOiling 93 pts. 37,399
• 3. dcrwheeler 86 pts. 37,331
• 4. Bruno Kestemont 80 pts. 37,274
• 5. ichwilldiesennamen 74 pts. 37,187
• 6. bravosk8erboy 68 pts. 37,171
• 7. grogar7 63 pts. 37,149
• 8. Bletchley Park 58 pts. 37,134
• 9. Dr. Goochie 53 pts. 37,109
• 10. akaaka 49 pts. 37,015

Comments

[LociOiling]

It's still pre-release, but based on the sequence shown here, this could be PDB 1XWR, 1ZPQ, or 8IGR. We'll see if the puzzle reveals more information when it's released.

[LociOiling]

The puzzle is live now, and it looks like 1ZPQ is a good match, based on the missing residues.

The link for 1ZPQ goes to the structure tab of the PDB page. It shows the sequence at the top of the display, starting with chain A. Any missing residues are greyed out. A dropdown lets you change the chain displayed.

AA Edit 3.0 shows the chains as they are found in the puzzle. That can be compared to what's shown on the structure tab.

For this puzzle, all four chains appear to have the same sequence, but the number of missing residues at the beginning and end is different for each. All together, the pattern of missing residues gives a unique fingerprint (probably unique, at least) that helps confirm a match between PDB and puzzle.

Here's what the display for chain C shows, with the missing residues highlighted in red:

Here's the dropdown or twirly in action:

[LociOiling]

Here's a manual alignment of the FASTA sequence (Display Files -> FASTA Sequence) for 1ZPQ and the AA Edit 3.0 output for puzzle 2663:

The PDB info is in uppercase, the AA Edit output is in lowercase. The PDB shows the same sequence for all four chains, so I just repeated that line four times.