1DRZ
| U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX | Descriptor: | MAGNESIUM ION, PROTEIN (U1 SMALL RIBONUCLEOPROTEIN A), RNA (HEPATITIS DELTA VIRUS GENOMIC RIBOZYME), ... | Authors: | Ferre-D'Amare, A.R, Zhou, K, Doudna, J.A. | Deposit date: | 1998-09-01 | Release date: | 1999-02-16 | Last modified: | 2021-11-03 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structure of a hepatitis delta virus ribozyme. Nature, 395, 1998
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1AN2
| RECOGNITION BY MAX OF ITS COGNATE DNA THROUGH A DIMERIC B/HLH/Z DOMAIN | Descriptor: | DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*TP*CP*AP*CP*GP*TP*GP*AP*CP*C P*TP*AP*CP*AP*C)- 3'), PROTEIN (TRANSCRIPTION FACTOR MAX (TF MAX)) | Authors: | Ferre-D'Amare, A.R, Prendergast, G.C, Ziff, E.B, Burley, S.K. | Deposit date: | 1996-09-06 | Release date: | 1997-09-17 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature, 363, 1993
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1AN4
| STRUCTURE AND FUNCTION OF THE B/HLH/Z DOMAIN OF USF | Descriptor: | DNA (5'-D(*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*C P*TP*AP*CP*A)-3'), DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*C P*GP*GP*GP*T)-3'), PROTEIN (UPSTREAM STIMULATORY FACTOR) | Authors: | Ferre-D'Amare, A.R, Pognonec, P, Roeder, R.G, Burley, S.K. | Deposit date: | 1997-03-15 | Release date: | 1997-09-17 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Structure and function of the b/HLH/Z domain of USF. EMBO J., 13, 1994
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4W90
| Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO | Descriptor: | (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide, MAGNESIUM ION, U1 small nuclear ribonucleoprotein A, ... | Authors: | Jones, C.P, Ferre-D'Amare, A.R. | Deposit date: | 2014-08-26 | Release date: | 2014-10-15 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (3.118 Å) | Cite: | Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. Embo J., 33, 2014
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4W92
| Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO | Descriptor: | (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide, 1,2-ETHANEDIOL, C-di-AMP ribsoswitch, ... | Authors: | Jones, C.P, Ferre-D'Amare, A.R. | Deposit date: | 2014-08-26 | Release date: | 2014-10-22 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (3.209 Å) | Cite: | Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. Embo J., 33, 2014
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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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7SXP
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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: | 2015-08-19 | 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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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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1M5K
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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
| 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
| 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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2Z75
| T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate | Descriptor: | 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose, MAGNESIUM ION, glmS ribozyme RNA, ... | Authors: | Klein, D.J, Wilkinson, S.R, Been, M.D, Ferre-D'Amare, A.R. | Deposit date: | 2007-08-15 | Release date: | 2007-09-04 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme J.Mol.Biol., 373, 2007
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2Z74
| T. tengcongensis glmS ribozyme bound to glucose-6-phosphate | Descriptor: | 6-O-phosphono-alpha-D-glucopyranose, MAGNESIUM ION, glmS ribozyme RNA, ... | Authors: | Klein, D.J, Wilkinson, S.R, Been, M.D, Ferre-D'Amare, A.R. | Deposit date: | 2007-08-15 | Release date: | 2007-09-04 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme J.Mol.Biol., 373, 2007
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6PQ7
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6WZS
| Fusibacterium ulcerans ZTP riboswitch bound to m-1-pyridinyl AICA | Descriptor: | 5-amino-1-(pyridin-3-yl)-1H-imidazole-4-carboxamide, Fusibacterium ulcerans ZTP riboswitch, MAGNESIUM ION, ... | Authors: | Pichling, P, Jones, C.P, Ferre-D'Amare, A.R, Tran, B. | Deposit date: | 2020-05-14 | Release date: | 2021-03-24 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (3.23 Å) | Cite: | Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design. Cell Chem Biol, 27, 2020
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6WZR
| Fusibacterium ulcerans ZTP riboswitch bound to p-1-pyridinyl AICA | Descriptor: | 5-amino-1-(pyridin-4-yl)-1H-imidazole-4-carboxamide, Fusibacterium ulcerans ZTP riboswitch, MAGNESIUM ION, ... | Authors: | Pichling, P, Jones, C.P, Ferre-D'Amare, A.R, Tran, B. | Deposit date: | 2020-05-14 | Release date: | 2021-03-24 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design. Cell Chem Biol, 27, 2020
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6PUQ
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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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1SB7
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6UP0
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6V9D
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6V9B
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1ZL3
| Coupling of active site motions and RNA binding | Descriptor: | 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FLO) UP*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3', SULFATE ION, tRNA pseudouridine synthase B | Authors: | Hoang, C, Hamilton, C.S, Mueller, E.G, Ferre-D'Amare, A.R. | Deposit date: | 2005-05-05 | Release date: | 2005-08-09 | Last modified: | 2023-08-23 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain Protein Sci., 14, 2005
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