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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

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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.