Placeholder image of a protein
Icon representing a puzzle

2690: Electron Density Reconstruction 145

Closed since 4 months ago

Novice Overall Prediction Electron Density

Summary

Created
November 11, 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. There are four of the a few different protein chains in this model, with several segments missing on each. Even with those residues it's a fairly large puzzle and so the trim tool will likely be needed.

Sequence
MSTSHVDDEDVNSIAVAKTDGLNQLYNLVAQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPLS MAHHHHHHMQKHNIKLNQNQDISQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERGIPITAEHAISTTTSAPSGDNKQSSSSDKK MYVASWQDYHSDFSEKYGDIALKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKLATWDKQGNLKY

Top groups

  1. Avatar for VeFold
    1. VeFold
    100 pts. 51,669
  2. Avatar for Go Science 2. Go Science 65 pts. 51,667
  3. Avatar for Contenders 3. Contenders 41 pts. 51,485
  4. Avatar for L'Alliance Francophone 4. L'Alliance Francophone 24 pts. 51,477
  5. Avatar for Anthropic Dreams 5. Anthropic Dreams 14 pts. 51,415
  6. Avatar for FamilyBarmettler 6. FamilyBarmettler 7 pts. 50,780
  7. Avatar for Australia 7. Australia 4 pts. 50,740
  8. Avatar for Void Crushers 8. Void Crushers 2 pts. 50,324
  9. Avatar for Marvin's bunch 9. Marvin's bunch 1 pt. 49,678
  10. Avatar for Gargleblasters 10. Gargleblasters 1 pt. 47,491
  1. Avatar for vybi 51. vybi Lv 1 2 pts. 46,294
  2. Avatar for jamiexq 52. jamiexq Lv 1 2 pts. 46,239
  3. Avatar for rosie4loop 53. rosie4loop Lv 1 1 pt. 45,808
  4. Avatar for Alistair69 54. Alistair69 Lv 1 1 pt. 45,743
  5. Avatar for DScott 55. DScott Lv 1 1 pt. 45,300
  6. Avatar for Mohoernchen 56. Mohoernchen Lv 1 1 pt. 45,281
  7. Avatar for p.naka 57. p.naka Lv 1 1 pt. 45,119
  8. Avatar for RWoodcock 58. RWoodcock Lv 1 1 pt. 45,085
  9. Avatar for akonin28 59. akonin28 Lv 1 1 pt. 44,786
  10. Avatar for orily1337 60. orily1337 Lv 1 1 pt. 44,615

Comments

Anfinsen_slept_here Lv 1

In case you were wondering…This appears to part of the ESCRT complex in yeast important for protein sorting and vesicle formation. A relevant PDB file is 2CAZ

LociOiling Lv 1

In addition to PDB 2CAZ, PDB 2F66 is also a close match. A PDB search using Foldit chain A returns a 100% match for both 2CAZ and 2F66.

Foldit chain C shows there is at least one difference. It starts with SDFSEK. 2F66 has SEFSKK at the same spot, but 2CAZ has SDFSEK.

In theory, Foldit chain F has the same sequence, but the SDFSEK part is missing, so both 2CAZ and 2F66 show a match.

Here's a manual alignment showing 2F66 on top, the two equivalent Foldit chains in the middle, then 2CAZ below. (I haven't yet compared them in detail, so there may be other differences.)

>2F66_3|Chains C, F|Protein SRN2|Saccharomyces cerevisiae (4932)
   ASWQDYHSEFSKKYGDIALKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKLATWDKQGNLKY
          SDFSEKYGDIALKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKL (Foldit C)
                     LKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKL (Foldit F)
MYVASWQDYHSDFSEKYGDIALKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKLATWDKQGNLKY
>2CAZ_3|Chains C, F|PROTEIN SRN2|SACCHAROMYCES CEREVISIAE (4932)

>2F66_2|Chains B, E|Vacuolar protein sorting-associated protein VPS28|Saccharomyces cerevisiae (4932)
                 GAMDISQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLERGIPITAEH
                              PLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERGIPIT (Foldit B)
                             VPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERGIPIT (Foldit E)
MAHHHHHHMQKHNIKLNQNQDISQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERGIPITAEHAISTTTSAPSGDNKQSSSSDKK
>2CAZ_2|Chains B, E|VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS28|SACCHAROMYCES CEREVISIAE (4932)

>2F66_1|Chains A, D|Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease|Saccharomyces cerevisiae (4932)
                 MTDGLNQLYNLVAQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPLS 
                     LNQLYNLVAQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITS     (Foldit A)
                     LNQLYNLVAQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPL   (Foldit D)
MSTSHVDDEDVNSIAVAKTDGLNQLYNLVAQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPLS
>2CAZ_1|Chains A, D|SUPPRESSOR PROTEIN STP22 OF TEMPERATURE-SENSITIVE ALPHA-FACTOR RECEPTOR AND ARGININE PERMEASE|SACCHAROMYCES CEREVISIAE (4932)

LociOiling Lv 1

Over in chat, beta_helix confirms:

This target is indeed 2CAZ. We can start posting the PDB codes along with each puzzle.

I forgot to mention that Saccharomyces cerevisiae, the natural source of this protein, is commonly known as brewer's yeast.