GGUAAAACAGCCUGUGGGUGAAACACA CCCACAGGGCCCAUUGGGCGCUAGCAC UCUGGUAUCACGGUACCUUUGUGCGCC UGUUUUACC
Puzzle: B3 cloverleaf RRE
Crystal structure kindly provided by: Deepak Koirala
Reference: Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element. Nat Commun 14: 1955-1955. (2023)
PDB id: 8dp3
]]>GCGGCGUUGCGUCCGAAAGUCUAAACAG ACACGGCCGCUUAAAAACAAAAGGAGA
Puzzle: NAD+ II riboswitch (another)
Crystal structure kindly provided by: Lin Huang
Reference: Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets. Nucleic Acids Res 51: 2904-2914 (2023)
PDB id: 8hb8
]]>GGAGCGUUACGUCCGAAAGUCGCAUUGCACU CCGCGACACGGCUCUUUAAAAACAAAAGGA
Puzzle: NAD+ II riboswitch
Crystal structure kindly provided by: Aiming Ren
Reference: Structure-based investigations of the NAD+-II riboswitch. Nucleic Acids Res 51: 54-67 (2023)
PDB id: 8gxc
]]>GGGGGCCACAGCAGAAGCGUUCACGUCGCGGCCCC UGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU
(Predict as dimer)
Puzzle: Chimpanzee CPEB3 HDV-like ribozyme
Crystal structure kindly provided by: BenoÎt Masquida
Reference: Anticodon-like loop-mediated dimerization in the crystal structures of HdV-like CPEB3 ribozymes. Biorxiv (2022)
PDB id: 7qr3
]]>GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCC UGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU
(Predict as dimer)
Puzzle: human CPEB3 HDV-like ribozyme
Crystal structure kindly provided by: BenoÎt Masquida
Reference: Anticodon-like loop-mediated dimerization in the crystal structures of HdV-like CPEB3 ribozymes. Biorxiv (2022)
PDB id: 7qr4
]]>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
]]>CGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGAA 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
Assessment of complex: raw prediction | Assessment results
Assessment of tBox: raw prediction | Assessment results
Assessment of tRNA: raw prediction | Assessment results
]]>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
Assessment of complex: raw prediction | Assessment results
Assessment of tBox: raw prediction | Assessment results
Assessment of tRNA: raw prediction | Assessment results
]]>tRNA:
GCGGAAGTAGTTCAGTGGTAGAACACCACCTTGCCAAGGTGGGGGTCGCGGG
TTCGAATCCCGTCTTCCGCTCCA
T-box:
GAAAGUGGGUGCGCGUUUGGCGCAUCAACUCGGGUGGAACCGCGGGA
GCUACGCUCUCGUCCCGAG
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
Assessment of complex: raw prediction | Assessment results
Assessment of tBox: raw prediction | Assessment results
Assessment of tRNA: raw prediction | Assessment results
]]>