A detailed time table for the “Unknown Rfam Puzzles” is available through google doc.
]]>A detailed time table for the “Unknown Rfam Puzzles” is available through google doc.
]]>Please feel free to contact Chichau if you have any question about RNA-Puzzles.
]]>Further, we have released the results of Puzzle 21, the Guanidine III Riboswitch.
Best Wishes!
Chichau
]]>GCGGGCUGACCGACCCCCCGAGUUCGCUCGGGGACAACUAGA CAUACAGUAUGAAAAUACUGAGCCCGC
Puzzle: methyl transferase ribozyme
Crystal structure kindly provided by: Lin Huang
Reference: Structure and mechanism of a methyltransferase ribozyme. Nat Chem Biol. (2022)
PDB id: 7v9e
]]>GGAGUAGAAGCGUUCAGCGGCCGAAAGGCCGCCCGGAAAUUGCUCC
Puzzle: xanthine riboswitch (Ideonella sp. B508-1)
Crystal structure kindly provided by: Aiming Ren
Reference: Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition. Nucleic Acids Res (2021)
]]>GGCGCACUGGCGCUGCGCCUUCGGGCGCCAAUCGUAGCGUGU CGGCGCC
Puzzle: Pepper Aptamer
Crystal structure kindly provided by: Aiming Ren
Reference: Structure-based investigation of fluorogenic Pepper aptamer. Nat Chem Biol (2021) 17: 1289-1295
PDB id: 7eoj
]]>GGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGAA ACACUGAUGUCGUAUACAGGGCG
Puzzle: PFSE in Sars-CoV-2
Crystal structure kindly provided by: Joseph A Piccirilli
Reference: The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 angstrom Using Chaperone-Assisted RNA Crystallography. ACS Chem Biol (2021) 16: 1469-1481
PDB id: 7mlx
]]>GAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGG AGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCG CGGG
Puzzle: human telomerase RNA
Crystal structure kindly provided by: Thi Hoang Duong Nguyen
Reference: Structure of human telomerase holoenzyme with bound telomeric DNA. Nature (2021) 593: 449-453
PDB id: 7bg9
]]>GGCUUCAACAACCCCGUAGGUUGGGCCGAAAGGCAGCGAAUCUACUGGAGCC
Puzzle: NAD+ riboswitch (Candidatus Koribacter versatilis Ellin345)
Crystal structure kindly provided by: Lin Huang
Reference: Structure and ligand binding of the ADP-binding domain of the NAD + riboswitch. RNA (2020) 26: 878-887
PDB id: 6tb7
]]>tRNA:
GGGCCUAUAGCUCAGGCGGUUAGAGCGCUUCGCUGAUAACGA
AGAGGUCGGAGGUUCGAGUCCUCCUAGGCCCACCA
T-box:
GGCGACGAUCCGGCCAUCACCGGGGAGCCUUCGGAAGAACGG
CGCCGCCGGAAACGGCGGCGCUCAGUAGAACCGAACGGGUGA
GCCCGUCACAGCUC
Puzzle: T-box riboswitch - tRNA complex (Nocardia farcinica ileS)
Crystal structure kindly provided by: Jingwei Zhang
Reference: High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove. Nat Struct Mol Biol. 2019 Dec;26(12):1114-1122. doi: 10.1038/s41594-019-0335-6. Epub 2019 Dec 2.
PDB id: 6ufm
raw prediction | Assessment results Complex T-box
]]>tRNA:
GCGGAAGTAGTTCAGTGGTAGAACACCACCTTGCCAAGGTGGG
GGTCGCGGGTTCGAATCCCGTCTTCCGCTCCA
T-box:
GUUGCAGUGAGAGAAAGAAGUACUUGCGUUUACCUCAUGAAAG
CGACCUUAGGGCGGUGUAAGCUAAGGAUGAGCACGCAACGAAA
GGCAUUCUUGAGCAAUUUUAAAAAAGAGGCUGGGAUUUUGUUC
UCAGCAACUAGGGUGGAACCGCGGGAGAACUCUCGUCCCUA
Puzzle: T-box riboswitch - tRNA complex (Bacillus subtilis glyQS)
Crystal structure kindly provided by: Jingwei Zhang
Reference: Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Nat Struct Mol Biol. 2019 Dec;26(12):1094-1105. doi: 10.1038/s41594-019-0326-7. Epub 2019 Nov 18.
PDB id: 6pom
raw prediction | Assessment results Complex T-box
]]>T-box:
GCGGAAGTAGTTCAGTGGTAGAACACCACCTTGCCAAGGTGG
GGGTCGCGGGTTCGAATCCCGTCTTCCGCTCCA
tRNA:
GAAAGUGGGUGCGCGUUUGGCGCAUCAACUCGGGUGGAACCG
CGGGAGCUACGCUCUCGUCCCGAG
Puzzle: T-box riboswitch - tRNA complex (Geobacillus kaustophilus glyQ)
Crystal structure kindly provided by: Jingwei Zhang
Reference: Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Nat Struct Mol Biol. 2019 Dec;26(12):1094-1105. doi: 10.1038/s41594-019-0326-7. Epub 2019 Nov 18.
PDB id: 6pmo
raw prediction | Assessment results Complex T-box
]]>GGGUGUAAUCUCCAAAAUAUGGUUGGGGAGCCUCCACCAGUGAA CCGUAAAAUCGCUGUCACCACCCAG
Puzzle: 2'-dG-II riboswitch
Crystal structure kindly provided by: Batey, R.T.
Reference: Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches. Nucleic Acids Res. 2019 Nov 18;47(20):10931-10941. doi: 10.1093/nar/gkz839.
PDB id: 6p2h
]]>GGACCUCGCAAGGGUAUCAUGGCGGACGACCGGGGUUCGAACCCCGGAUC
CGGCCGUCCGCCGUGAUCCAUGCGGUUACCGCCCGCGUGUCGAACCCAGG
UGUGCGAGGUCC
Puzzle: adenovirus virus-associated RNA
Crystal structure kindly provided by: Jingwei Zhang
Reference: Crystal structure of an adenovirus virus-associated RNA. Nature Communicationsvolume 10, Article number: 2871 (2019).
PDB id: 6ol3
]]>GUACGAAGGAAGGUUUGGUAUGGGGUAGUUGUCGUAC
Puzzle: Mango-III aptamer
Crystal structure kindly provided by: Ferre-D'Amare, A.R.
Reference: Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Nat Chem Biol. 2019 May;15(5):472-479. doi: 10.1038/s41589-019-0267-9. Epub 2019 Apr 15.
PDB id: 6e8u
]]>UUACUGUGAGAAUCAGUAACAAACAUGUGGGGCUUAUAU CUAAUCGAAAGAUUAGUAUUAGUGCAGAC
GUUAAAACCAUGUC
Puzzle: Hatchet Ribozyme
Crystal structure kindly provided by: Aiming Ren
Reference: Hatchet ribozyme structure and implications for cleavage mechanism. Proc Natl Acad Sci U S A. 2019 May 28;116(22):10783-10791. doi: 10.1073/pnas.1902413116. Epub 2019 May 14.
raw prediction | Assessment results monomer dimer
]]>CCGGACGAGGUGCGCCGUACCCGGUCAGGACAAGACGGCGC
Puzzle: Guanidine III Riboswitch
Crystal structure kindly provided by: David M J Lilley
Reference: Structure of the Guanidine III Riboswitch. Cell Chem Biol. 2017 Nov 16;24(11):1407-1415.e2. doi: 10.1016/j.chembiol.2017.08.021. Epub 2017 Oct 5.
]]>Puzzle: Another Twister Sister ribozyme
Crystal structure kindly provided by: Amy Ren
Reference: Zheng, L., Mairhofer, E., Teplova, M., Zhang, Y., Ma, J., Patel, D.J., Micura, R., Ren, A. Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme. (2017) Nat Commun 8: 1180-1180
]]>