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
| 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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8F5G
| NusG-RNA complex | Descriptor: | DI(HYDROXYETHYL)ETHER, RNA, Transcription termination/antitermination protein NusG | Authors: | Elghondakly, A.T, Ferre-D'Amare, A.R. | Deposit date: | 2022-11-14 | Release date: | 2023-11-22 | Last modified: | 2024-09-25 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Major-groove sequence-specific RNA recognition by LoaP, a paralog of transcription elongation factor NusG. Structure, 32, 2024
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8FI8
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8FHZ
| Structure of Lettuce aptamer 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, Lettuce DNA aptamer, MAGNESIUM ION, ... | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-12-15 | Release date: | 2023-05-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Intricate 3D architecture of a DNA mimic of GFP. Nature, 618, 2023
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8FHV
| Structure of Lettuce aptamer bound to DFHBI-1T with thallium I ions | Descriptor: | (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one, Lettuce DNA aptamer, MAGNESIUM ION, ... | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-12-15 | Release date: | 2023-05-10 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Intricate 3D architecture of a DNA mimic of GFP. Nature, 618, 2023
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8FI2
| Structure of Lettuce C20T 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, Lettuce DNA aptamer, MAGNESIUM ION, ... | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-12-15 | Release date: | 2023-05-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Intricate 3D architecture of a DNA mimic of GFP. Nature, 618, 2023
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8FI1
| Structure of Lettuce C20G 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, Lettuce DNA aptamer, MAGNESIUM ION, ... | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-12-15 | Release date: | 2023-05-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Intricate 3D architecture of a DNA mimic of GFP. Nature, 618, 2023
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8FI0
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8FI7
| Structure of Lettuce C20T 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, Lettuce DNA aptamer, MAGNESIUM ION, ... | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-12-15 | Release date: | 2023-05-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Intricate 3D architecture of a DNA mimic of GFP. Nature, 618, 2023
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8FHX
| Structure of Lettuce aptamer 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, Lettuce DNA aptamer, MAGNESIUM ION, ... | Authors: | Passalacqua, L.F.M, Ferre-D'Amare, A.R. | Deposit date: | 2022-12-15 | Release date: | 2023-05-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Intricate 3D architecture of a DNA mimic of GFP. Nature, 618, 2023
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6UP0
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6V9D
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6V9B
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1NU4
| U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix | Descriptor: | MAGNESIUM ION, MALONIC ACID, U1A RNA binding domain | Authors: | Rupert, P.B, Xiao, H, Ferre-D'Amare, A.R. | Deposit date: | 2003-01-30 | Release date: | 2003-02-14 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | U1A RNA-binding domain at 1.8 A resolution. Acta Crystallogr.,Sect.D, 59, 2003
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4NYC
| Crystal structure of the E. coli thiM riboswitch in complex with thieno[2,3-b]pyrazin-7-amine | Descriptor: | MAGNESIUM ION, MANGANESE (II) ION, thiM TPP riboswitch, ... | Authors: | Warner, K.D, Homan, P, Weeks, K.M, Smith, A.G, Abell, C, Ferre-D'Amare, A.R. | Deposit date: | 2013-12-10 | Release date: | 2014-06-04 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically. Chem.Biol., 21, 2014
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4NYA
| Crystal structure of the E. coli thiM riboswitch in complex with 5-(azidomethyl)-2-methylpyrimidin-4-amine | Descriptor: | 5-(azidomethyl)-2-methylpyrimidin-4-amine, MAGNESIUM ION, thiM TPP riboswitch | Authors: | Warner, K.D, Homan, P, Weeks, K.M, Smith, A.G, Abell, C, Ferre-D'Amare, A.R. | Deposit date: | 2013-12-10 | Release date: | 2014-06-04 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically. Chem.Biol., 21, 2014
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4NYD
| Crystal structure of the E. coli thiM riboswitch in complex with hypoxanthine | Descriptor: | HYPOXANTHINE, MAGNESIUM ION, MANGANESE (II) ION, ... | Authors: | Warner, K.D, Homan, P, Weeks, K.M, Smith, A.G, Abell, C, Ferre-D'Amare, A.R. | Deposit date: | 2013-12-10 | Release date: | 2014-06-04 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically. Chem.Biol., 21, 2014
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4NYB
| Crystal structure of the E. coli thiM riboswitch in complex with (4-(1,2,3-thiadiazol-4-yl)phenyl)methanamine | Descriptor: | 1-[4-(1,2,3-thiadiazol-4-yl)phenyl]methanamine, MAGNESIUM ION, MANGANESE (II) ION, ... | Authors: | Warner, K.D, Homan, P, Weeks, K.M, Smith, A.G, Abell, C, Ferre-D'Amare, A.R. | Deposit date: | 2013-12-10 | Release date: | 2014-06-04 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically. Chem.Biol., 21, 2014
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4NYG
| Crystal structure of the E. coli thiM riboswitch in complex with thiamine | Descriptor: | 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM, MAGNESIUM ION, thiM TPP riboswitch | Authors: | Warner, K.D, Homan, P, Weeks, K.M, Smith, A.G, Abell, C, Ferre-D'Amare, A.R. | Deposit date: | 2013-12-10 | Release date: | 2014-06-04 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (3.05 Å) | Cite: | Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically. Chem.Biol., 21, 2014
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5V3F
| Co-crystal structure of the fluorogenic RNA Mango | Descriptor: | 4-{[(2S)-3-{2,16-dioxo-20-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-2,3-dihydro-1,3-benzothiazol-2-yl]methyl}-1-methylquinolin-1-ium, PHOSPHATE ION, POTASSIUM ION, ... | Authors: | Trachman, R.J, Ferre-D'Amare, A.R. | Deposit date: | 2017-03-07 | Release date: | 2017-05-24 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nat. Chem. Biol., 13, 2017
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6CB3
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6CC3
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6C65
| Crystal Structure of the Mango-II-A22U Fluorescent Aptamer Bound to TO1-Biotin | Descriptor: | 4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium, POTASSIUM ION, RNA (35-MER), ... | Authors: | Trachman, R.J, Ferre-D'Amare, A.R. | Deposit date: | 2018-01-17 | Release date: | 2018-08-08 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.80005169 Å) | Cite: | Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness. Biochemistry, 57, 2018
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6CC1
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