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2741: Electron Density Reconstruction 162

Closed since 17 days ago

Novice Novice Overall Overall Prediction Prediction Electron Density Electron Density

Summary

Created
March 11, 2026
Expires
Max points
100
Description

The structure of this protein-DNA complex 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 comes from PDB entry 2NRE.

Sequence
MSDQQQPPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD GCCGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCA

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Comments

BootsMcGraw Lv 1

Why does the DNA look like cooked spaghetti, and not a nice double-helix?

spvincent Lv 1

I think it's RNA rather than DNA (tab reveals Uracil rather than Thymine). And RNA structures tend to rather messier than the clean-looking double helices DNA tends to form. From the PDB entry it looks like this is part of a tRNA molecule which have various weird loops and non-standard nucleotides.

horowsah Staff Lv 1

Yep, RNA- and RNA takes all sorts of shapes as it performs a variety of functions.