Completed puzzles (34)
Puzzle PZ4
Description
SAM-I riboswitch aptamer.
RNA sequence (5' to 3')
GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCACUAGU CUAGCGUCAGCUUCGGCUGACGCUAGGCUAGUGGUGCCAAUUCCUGCAGCGGAA ACGUUGAAAGAUGAGCCA
Experimental structure(s)
solutionPZ4.pdb solutionPZ4_1.pdb
References

N. J. Baird, J. Zhang, T. Hamma and A. R. Ferre-DAmare (2012). YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA 18: 759-770.

PDB ID:
3v7e
Opening date:
19 Oct 2020, 23:24
Closing date (Human category):
19 Oct 2020, 23:24
Puzzle PZ3
Description
The crystallized sequence was slightly different (an apical loop was replaced by a GAAA loop) but it was not mentioned to protect the crystallographers.
RNA sequence (5' to 3')
CUCUGGAGAGAACCGUUUAAUCGGUCGCCGAAGGAGCAAGCUCUGCGCAUAUGC AGAGUGAAACUCUCAGGCAAAAGGACAGAG
Experimental structure(s)
solutionPZ3.pdb solutionPZ3_1.pdb
References

L. Huang, A. Serganov and D.J. Patel (2010). Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch. Mol. Cell. 40: 774-786.

PDB ID:
3owz
Opening date:
19 Oct 2020, 23:24
Closing date (Human category):
19 Oct 2020, 23:24
Puzzle PZ2
Description
The crystal structure shows a 100 nt square that assembles from four inner and four outer strands. The secondary structure shown was used for the design of the square. Actual base pairing in the crystal may deviate. 3D coordinates of the nucleotides in the inner strands (B,D,F,H) were provided. What are the structures of the outer strands (A,C,E,G)?
RNA sequence (5' to 3')
CCGGAGGAACUACUG-CCGGCAGCCU-CCGGAGGAACUACUG-CCGGCAGCCU-CCGGAGGAACUACUG-CCGGCAGCCU-CCGGAGGAACUACUG-CCGGCAGCCU
Experimental structure(s)
solutionPZ2.pdb
References

S.M. Dibrov, J. McLean, J. Parsons and T. Hermann (2011). Self-assembling RNA square. PNAS 108: 6405-6408.

PDB ID:
3p59
Opening date:
19 Oct 2020, 23:24
Closing date (Human category):
19 Oct 2020, 23:24
Puzzle PZ1
Description
knowing that the crystal structure shows a homodimer that contains two strands of the sequence. The strands hybridize with blunt ends (C-G closing base pairs).
RNA sequence (5' to 3')
CCGCCGCGCCAUGCCUGUGGCGG
Experimental structure(s)
solutionPZ1.pdb
References

S.M. Dibrov, J. McLean and T. Hermann (2011). Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA, Acta Cryst. D, Biological Crystallography 67: 97-104.

PDB ID:
3mei
Opening date:
19 Oct 2020, 23:24
Closing date (Human category):
19 Oct 2020, 23:24