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1DRZ
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BU of 1drz by Molmil
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
1AN2
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BU of 1an2 by Molmil
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
1AN4
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BU of 1an4 by Molmil
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
4W90
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BU of 4w90 by Molmil
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
4W92
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BU of 4w92 by Molmil
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
6C65
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BU of 6c65 by Molmil
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
7SXP
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BU of 7sxp by Molmil
G-quadruplex structure formed in the NRAS mRNA with a G8U substitution
Descriptor: CACODYLIC ACID, NRAS mRNA, POTASSIUM ION
Authors:Banco, M.T, Ferre-D'Amare, A.R.
Deposit date:2021-11-24
Release date:2023-05-31
Last modified:2023-07-05
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Investigating the NRAS 5' UTR as a target for small molecules.
Cell Chem Biol, 30, 2023
4XK0
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BU of 4xk0 by Molmil
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
4XNR
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BU of 4xnr by Molmil
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
1M5K
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BU of 1m5k by Molmil
Crystal structure of a hairpin ribozyme in the catalytically-active conformation
Descriptor: CALCIUM ION, CHLORIDE ION, PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A), ...
Authors:Rupert, P.B, Ferre-D'Amare, A.R.
Deposit date:2002-07-09
Release date:2002-08-02
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Transition state stabilization by a catalytic RNA
Science, 298, 2002
1M5V
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BU of 1m5v by Molmil
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
1M5O
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BU of 1m5o by Molmil
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
1M5P
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BU of 1m5p by Molmil
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
2Z75
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BU of 2z75 by Molmil
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
2Z74
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BU of 2z74 by Molmil
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
6PQ7
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BU of 6pq7 by Molmil
Structure of the iMango-III fluorescent aptamer at room temperature.
Descriptor: MAGNESIUM ION, POTASSIUM ION, RNA (37-MER), ...
Authors:Trachman III, R.J, Ferre-D'Amare, A.R.
Deposit date:2019-07-08
Release date:2019-07-31
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (3 Å)
Cite:Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser.
Acta Crystallogr.,Sect.F, 75, 2019
6WZS
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BU of 6wzs by Molmil
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
6WZR
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BU of 6wzr by Molmil
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
6PUQ
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BU of 6puq by Molmil
1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN
Descriptor: ACETATE ION, DI(HYDROXYETHYL)ETHER, FLAVIN MONONUCLEOTIDE, ...
Authors:Sjekloca, L, Ferre-D'Amare, A.R.
Deposit date:2019-07-18
Release date:2020-07-22
Last modified:2022-06-22
Method:X-RAY DIFFRACTION (1.56 Å)
Cite:Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN.
MicroPubl Biol, 2022, 2022
1NU4
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BU of 1nu4 by Molmil
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
1SB7
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BU of 1sb7 by Molmil
Crystal structure of the E.coli pseudouridine synthase TruD
Descriptor: GLYCEROL, PHOSPHATE ION, tRNA pseudouridine synthase D
Authors:Hoang, C, Ferre-D'Amare, A.R.
Deposit date:2004-02-10
Release date:2004-06-29
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold.
Rna, 10, 2004
6UP0
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BU of 6up0 by Molmil
Structure of the Mango-III fluorescent aptamer bound to YO3-Biotin
Descriptor: MAGNESIUM ION, Mango-III fluorescent aptamer, POTASSIUM ION, ...
Authors:Trachman, R.J, Ferre-D'Amare, A.R.
Deposit date:2019-10-16
Release date:2020-10-21
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.
Rna, 27, 2021
6V9D
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BU of 6v9d by Molmil
Co-crystal structure of the fluorogenic Mango-IV homodimer bound to TO1-Biotin
Descriptor: 2-[(E)-(1-methylquinolin-4(1H)-ylidene)methyl]-3-(2-oxopropyl)-1,3-benzothiazol-3-ium, BROMIDE ION, POTASSIUM ION, ...
Authors:Trachman, R.J, Ferre-D'Amare, A.R.
Deposit date:2019-12-13
Release date:2020-05-20
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair.
Structure, 28, 2020
6V9B
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BU of 6v9b by Molmil
Co-crystal structure of the fluorogenic Mango-IV homodimer bound to TO1-Biotin
Descriptor: POTASSIUM ION, RNA (28-MER), ~{N}-methyl-2-[2-[(~{E})-(1-methylquinolin-4-ylidene)methyl]-1,3-benzothiazol-3-yl]ethanamide
Authors:Trachman, R.J, Ferre-D'Amare, A.R.
Deposit date:2019-12-13
Release date:2020-05-20
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair.
Structure, 28, 2020
1ZL3
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BU of 1zl3 by Molmil
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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