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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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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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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7SXP
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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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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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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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2APO
 | | Crystal Structure of the Methanococcus jannaschii Cbf5 Nop10 Complex | | Descriptor: | POTASSIUM ION, Probable tRNA pseudouridine synthase B, Ribosome biogenesis protein Nop10, ... | | Authors: | Hamma, T, Reichow, S.L, Varani, G, Ferre-D'Amare, A.R. | | Deposit date: | 2005-08-16 | | Release date: | 2005-11-15 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs.
Nat.Struct.Mol.Biol., 12, 2005
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2AQA
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2AQC
 | | NMR Structural analysis of archaeal Nop10 | | Descriptor: | Ribosome biogenesis protein Nop10, ZINC ION | | Authors: | Hamma, T, Reichow, S.L, Varani, G, Ferre-D'Amare, A.R. | | Deposit date: | 2005-08-17 | | Release date: | 2005-11-15 | | Last modified: | 2022-03-09 | | Method: | SOLUTION NMR | | Cite: | The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs.
Nat.Struct.Mol.Biol., 12, 2005
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3IWN
 | | Co-crystal structure of a bacterial c-di-GMP riboswitch | | Descriptor: | 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one), C-di-GMP riboswitch, U1 small nuclear ribonucleoprotein A | | Authors: | Kulshina, N, Baird, N.J, Ferre-D'Amare, A.R. | | Deposit date: | 2009-09-02 | | Release date: | 2009-11-10 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.
Nat.Struct.Mol.Biol., 16, 2009
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3K1V
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3K0J
 | | Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module | | Descriptor: | MAGNESIUM ION, RNA (87-MER), THIAMINE DIPHOSPHATE, ... | | Authors: | Kulshina, N, Edwards, T.E, Ferre-D'Amare, A.R. | | Deposit date: | 2009-09-24 | | Release date: | 2009-12-22 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch.
Rna, 16, 2010
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4LCK
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4TZW
 | | Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and replacing Mg2+ with Sr2+ post crystallization | | Descriptor: | Ribosome-associated protein L7Ae-like, STRONTIUM ION, T-box Stem I, ... | | Authors: | Zhang, J, Ferre-D'Amare, A.R. | | Deposit date: | 2014-07-11 | | Release date: | 2014-09-10 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (4.671 Å) | | Cite: | Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
Structure, 22, 2014
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4TZP
 | | As Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF protein | | Descriptor: | Ribosome-associated protein L7Ae-like, engineered tRNA, glyQ T-box Stem I | | Authors: | Zhang, J, Ferre-D'Amare, A.R. | | Deposit date: | 2014-07-10 | | Release date: | 2014-09-10 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (8.503 Å) | | Cite: | Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
Structure, 22, 2014
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4TZV
 | | Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallization | | Descriptor: | Ribosome-associated protein L7Ae-like, T-box stem I, engineered tRNA | | Authors: | Zhang, J, Ferre-D'Amare, A.R. | | Deposit date: | 2014-07-11 | | Release date: | 2014-09-10 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (5.03 Å) | | Cite: | Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
Structure, 22, 2014
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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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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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