2675: Electron Density Reconstruction 140

Closed since 5 months ago

Summary

• Created: October 07, 2025
• Expires: October 23, 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 a large protein, and a small bit of DNA, and the Trim tool is highly recommended.

• Sequence: CATTAGAA TCTAATG MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE

Top groups

• 11. SETI.Germany 1 pt. 36,262
• 12. Russian team 1 pt. 35,405
• 13. Eὕρηκα! Heureka! 1 pt. 34,242

Top soloists

• 21. TheGUmmer 18 pts. 38,222
• 22. AlkiP0Ps 16 pts. 38,130
• 23. NinjaGreg 15 pts. 38,066
• 24. BarrySampson 13 pts. 37,882
• 25. Anfinsen_slept_here 12 pts. 37,880
• 26. spvincent 11 pts. 37,856
• 27. georg137 9 pts. 37,606
• 28. jausmh 8 pts. 37,567
• 29. zxspectrum 8 pts. 37,342
• 30. alcor29 7 pts. 37,337

Comments

[LociOiling]

This week's puzzle includes DNA, and the protein part is pucker-free.

There are lots of matches for this protein, a DNA polymerase. There's a long series starting with 1ZQA and stretching to 1ZQT, which match both the DNA and the protein parts.

Unfortunately, at quick glance, all the entries in that range seem to start with "TLNGG", where the puzzle protein has begins "ETLNGG". So it's again a question of missing residues, those 1ZQ* entries seem to be missing one residue that the Foldit puzzle has, although I haven't inspected the entire list.

I will try to refine the search, the PDB assures me there are 678 matches for the protein part….

[LociOiling]

After further consideration, it seems like the series that runs 1ZQA and to 1ZQT is indeed a match for this puzzle.

It turns out that there are missing residues, then there are zero occupancy residues. The glutamate that appears as segment 1 in Foldit is listed as zero occupancy for 1ZQA. The PDB file tells the story.

First, there are the missing residues, which don't include that glutamate (GLU):

REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     MET A     1                                                      
REMARK 465     SER A     2                                                      
REMARK 465     LYS A     3                                                      
REMARK 465     ARG A     4                                                      
REMARK 465     LYS A     5                                                      
REMARK 465     ALA A     6                                                      
REMARK 465     PRO A     7                                                      
REMARK 465     GLN A     8      

But then there are a couple of zero occupancy residues, both glutamate as it happens:

REMARK 475 ZERO OCCUPANCY RESIDUES                                              
REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY.             
REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT                
REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;                      
REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE)          
REMARK 475   M RES C  SSEQI                                                     
REMARK 475     GLU A     9                                                      
REMARK 475     GLU A   247     

The PDB structure tab grays out the zero occupancy residues along with the missing residues in its sequence display:

So there are eight missing residues plus the zero occupancy glutamate grayed out at the start, and then a single glutamate grayed in the middle, between 241 and 251.

Foldit, on the other hand, simply includes the doubtful glutamates in the puzzle, since they do have x-y-z coordinates in the PDB file, where the missing residues do not. That makes sense; even though the exact coordinates are doubtful, Foldit has tools to find a better spot for each residue.

What's odd is that the entire 1ZQA to 1ZQT series has the same set of missing and zero occupancy residues. There are some additional series from the same authors where each likewise has the same missing/zero residues. So there's still no easy way to determine which of the PDB entries was used for the Foldit puzzle.