7KVV
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![BU of 7kvv by Molmil](/molmil-images/mine/7kvv) | Crystal structure of Squash RNA aptamer in complex with DFHBI-1T | Descriptor: | (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one, MAGNESIUM ION, Squash RNA aptamer bound to DFHO | Authors: | Truong, L, Ferre-D'Amare, A.R. | Deposit date: | 2020-11-28 | Release date: | 2022-01-19 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat.Chem.Biol., 18, 2022
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3FU2
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![BU of 3fu2 by Molmil](/molmil-images/mine/3fu2) | |
8EYW
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![BU of 8eyw by Molmil](/molmil-images/mine/8eyw) | Beetroot dimer bound to ThT | Descriptor: | 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium, POTASSIUM ION, RNA (49-MER) | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-10-28 | Release date: | 2023-05-31 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun, 14, 2023
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8EYU
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![BU of 8eyu by Molmil](/molmil-images/mine/8eyu) | Structure of Beetroot dimer bound to DFAME | Descriptor: | POTASSIUM ION, RNA (49-MER), methyl (2E)-3-{(4Z)-4-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-1-methyl-5-oxo-4,5-dihydro-1H-imidazol-2-yl}prop-2-enoate | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-10-28 | Release date: | 2023-05-31 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun, 14, 2023
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8EYV
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![BU of 8eyv by Molmil](/molmil-images/mine/8eyv) | Structure of Beetroot dimer bound to DFHO | Descriptor: | (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one, POTASSIUM ION, RNA (45-MER) | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-10-28 | Release date: | 2023-05-31 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun, 14, 2023
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8F0N
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![BU of 8f0n by Molmil](/molmil-images/mine/8f0n) | Wobble Beetroot (A16U-U38G) dimer bound to DFHO | Descriptor: | (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one, POTASSIUM ION, RNA (49-MER) | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-11-03 | Release date: | 2023-05-31 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun, 14, 2023
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7LYJ
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![BU of 7lyj by Molmil](/molmil-images/mine/7lyj) | SARS-CoV-2 frameshifting pseudoknot RNA | Descriptor: | IRIDIUM HEXAMMINE ION, MAGNESIUM ION, POTASSIUM ION, ... | Authors: | Jones, C.P, Ferre-D'Amare, A.R. | Deposit date: | 2021-03-07 | Release date: | 2021-05-26 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (2.11 Å) | Cite: | Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot. Rna, 28, 2022
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3FS0
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![BU of 3fs0 by Molmil](/molmil-images/mine/3fs0) | |
7L0Z
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![BU of 7l0z by Molmil](/molmil-images/mine/7l0z) | Spinach variant bound to DFHBI-1T | Descriptor: | (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one, MAGNESIUM ION, PHOSPHATE ION, ... | Authors: | Truong, L, Trachman, R.J, Ferre-D'Amare, A.R. | Deposit date: | 2020-12-13 | Release date: | 2021-05-26 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET. Rna, 27, 2021
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7KVT
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![BU of 7kvt by Molmil](/molmil-images/mine/7kvt) | Crystal structure of Squash RNA aptamer in complex with DFHBI-1T with iridium (III) ions | Descriptor: | (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one, IRIDIUM HEXAMMINE ION, MAGNESIUM ION, ... | Authors: | Truong, L, Ferre-D'Amare, A.R. | Deposit date: | 2020-11-28 | Release date: | 2022-01-19 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (2.73 Å) | Cite: | The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat.Chem.Biol., 18, 2022
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7KVU
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![BU of 7kvu by Molmil](/molmil-images/mine/7kvu) | Crystal structure of Squash RNA aptamer in complex with DFHBI-1T | Descriptor: | (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one, MAGNESIUM ION, POTASSIUM ION, ... | Authors: | Truong, L, Ferre-D'Amare, A.R. | Deposit date: | 2020-11-28 | Release date: | 2022-01-19 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.68 Å) | Cite: | The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat.Chem.Biol., 18, 2022
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3EGZ
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![BU of 3egz by Molmil](/molmil-images/mine/3egz) | Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch | Descriptor: | 7-CHLOROTETRACYCLINE, MAGNESIUM ION, Tetracycline aptamer and artificial riboswitch, ... | Authors: | Xiao, H, Edwards, T.E, Ferre-D'Amare, A.R. | Deposit date: | 2008-09-11 | Release date: | 2008-10-28 | Last modified: | 2021-10-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch Chem.Biol., 15, 2008
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1M5K
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![BU of 1m5k by Molmil](/molmil-images/mine/1m5k) | |
1M5V
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![BU of 1m5v by Molmil](/molmil-images/mine/1m5v) | Transition State Stabilization by a Catalytic RNA | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, RNA HAIRPIN RIBOZYME, ... | Authors: | Rupert, P.B, Massey, A.P, Sigurdsson, S.T, Ferre-D'Amare, A.R. | Deposit date: | 2002-07-09 | Release date: | 2002-10-12 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Transition state stabilization by a catalytic RNA Science, 298, 2002
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1M5O
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![BU of 1m5o by Molmil](/molmil-images/mine/1m5o) | Transition State Stabilization by a Catalytic RNA | Descriptor: | CALCIUM ION, RNA SUBSTRATE, RNA HAIRPIN RIBOZYME, ... | Authors: | Rupert, P.B, Massey, A.P, Sigurdsson, S.T, Ferre-D'Amare, A.R. | Deposit date: | 2002-07-09 | Release date: | 2002-10-12 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Transition state stabilization by a catalytic RNA Science, 298, 2002
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1M5P
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![BU of 1m5p by Molmil](/molmil-images/mine/1m5p) | Transition State Stabilization by a Catalytic RNA | Descriptor: | CALCIUM ION, RNA HAIRPIN RIBOZYME, RNA INHIBITOR SUBSTRATE, ... | Authors: | Rupert, P.B, Massey, A, Sigurdsson, S.T, Ferre-D'Amare, A.R. | Deposit date: | 2002-07-09 | Release date: | 2002-10-12 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Transition state stabilization by a catalytic RNA Science, 298, 2002
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4XNR
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![BU of 4xnr by Molmil](/molmil-images/mine/4xnr) | Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized by Position-selective Labeling of RNA (PLOR), in Complex with Adenine | Descriptor: | ADENINE, MAGNESIUM ION, Vibrio Vulnificus Adenine Riboswitch | Authors: | Zhang, J, Liu, Y, Wang, Y.-X, Ferre-D'Amare, A.R. | Deposit date: | 2015-01-16 | Release date: | 2015-05-06 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.21 Å) | Cite: | Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature, 522, 2015
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7MKY
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![BU of 7mky by Molmil](/molmil-images/mine/7mky) | SARS-CoV-2 frameshifting pseudoknot RNA | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, COBALT HEXAMMINE(III), MAGNESIUM ION, ... | Authors: | Jones, C.P, Ferre-D'Amare, A.R. | Deposit date: | 2021-04-27 | Release date: | 2021-05-26 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.31 Å) | Cite: | Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot. Rna, 28, 2022
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6UP0
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![BU of 6up0 by Molmil](/molmil-images/mine/6up0) | |
4XK0
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![BU of 4xk0 by Molmil](/molmil-images/mine/4xk0) | Crystal structure of a tetramolecular RNA G-quadruplex in potassium | Descriptor: | BARIUM ION, POTASSIUM ION, RNA (5'-(*UP*GP*GP*GP*GP*U)-3') | Authors: | Chen, M.C, Murat, P, Abecassis, K.A, Ferre-D'Amare, A.R, Balasubramanian, S. | Deposit date: | 2015-01-09 | Release date: | 2015-02-11 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (1.08 Å) | Cite: | Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase. Nucleic Acids Res., 43, 2015
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6V9B
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![BU of 6v9b by Molmil](/molmil-images/mine/6v9b) | |
3V7E
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![BU of 3v7e by Molmil](/molmil-images/mine/3v7e) | Crystal structure of YbxF bound to the SAM-I riboswitch aptamer | Descriptor: | COBALT HEXAMMINE(III), MAGNESIUM ION, Ribosome-associated protein L7Ae-like, ... | Authors: | Baird, N.J, Zhang, J, Hamma, T, Ferre-D'Amare, A.R. | Deposit date: | 2011-12-21 | Release date: | 2012-03-07 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. Rna, 18, 2012
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6V9D
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3V7Q
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![BU of 3v7q by Molmil](/molmil-images/mine/3v7q) | Crystal structure of B. subtilis YlxQ at 1.55 A resolution | Descriptor: | CITRIC ACID, POTASSIUM ION, Probable ribosomal protein ylxQ | Authors: | Baird, N.J, Zhang, J, Hamma, T, Ferre-D'Amare, A.R. | Deposit date: | 2011-12-21 | Release date: | 2012-03-07 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. Rna, 18, 2012
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4TS2
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![BU of 4ts2 by Molmil](/molmil-images/mine/4ts2) | Crystal structure of the Spinach RNA aptamer in complex with DFHBI, magnesium ions | Descriptor: | (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one, MAGNESIUM ION, POTASSIUM ION, ... | Authors: | Warner, K.D, Chen, M.C, Song, W, Strack, R.L, Thorn, A, Jaffrey, S.R, Ferre-D'Amare, A.R. | Deposit date: | 2014-06-18 | Release date: | 2014-07-23 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.884 Å) | Cite: | Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat.Struct.Mol.Biol., 21, 2014
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