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2344: Electron Density Reconstruction 54 (Trim tool recommended)

Closed since over 2 years ago

Novice Overall Prediction Electron Density

Summary

Created
August 21, 2023
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 one has a big protein chain and then two smaller protein chains as well. Also, it's pretty gigantic, so the Trim Tool is highly recommended.

Sequence
KKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWGRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLREKVSELHPAIAKL TDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYIKGILK ETFSKIRVKPEHVIGVTVAFVIIEAILTYGRF

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  1. Avatar for Fboar 61. Fboar Lv 1 1 pt. 0
  2. Avatar for Erikas Blazukas 62. Erikas Blazukas Lv 1 1 pt. 0
  3. Avatar for Swapper242 63. Swapper242 Lv 1 1 pt. 0
  4. Avatar for AlphaFold2 64. AlphaFold2 Lv 1 1 pt. 0
  5. Avatar for badgoes 65. badgoes Lv 1 1 pt. 0

Comments

Artoria2e5 Lv 1

This is the SecYEG translocon of Methanocaldococcus jannaschii. There are multiple PDB structures of this complex and I don't know which one this is.

AA Edit dumps

>A
kklipilekipevelpvkeitfkeklkwtgivlvlyfimgcidvytagaqipaifefwgrigtlitlgigpivtagiimqllvgsgiiqmdlsipenralfqgcqkllsiimcfveavlfvgagafgiltpllaflviiqiafgsiiliyldeivskygigsgiglfiaagvsqtifvgalgpegylwkflnsliqgvpnieyiapiigtiivflmvvyaecmrveiplahgrikgavgkypikfvyvsnipvilaaalfaniqlwglalyrmgipilghyeggravdgiayylstpyglssvisdpihaivymiamiitcvmfgifwvettgldpksmakrigslgmaikgfrksekaiehrlkryippltvmssafvgflatianfigalgggtgvlltvsivyrmyeqllrekvselhpaiakl
>B
tdfnqkieqlkefieecrrvwlvlkkptkdeylavakvtalgisllgiigyiihvpatyikgilk
>C
etfskirvkpehvigvtvafviieailtygrf

Blasting A gives an exact match at 2YXQ, which has no unmodelled residues in-between. Good!

Oh, and don't worry too much about burials. A good chunk of this thing sits in a lipid membrane.