PDB: 79225 resultsInfo pagesStatus searchChemie searchBIRD

---

2D2K	Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme Descriptor: 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', ... Authors: Alam, S, Grum-Tokars, V, Krucinska, J, Kundracik, M.L, Wedekind, J.E. Deposit date: 2005-09-11 Release date: 2005-11-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.65 Å) Cite: Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn Biochemistry, 44, 2005
2D2L	Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39 Descriptor: 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', ... Authors: Alam, S, Grum-Tokars, V, Krucinska, J, Kundracik, M.L, Wedekind, J.E. Deposit date: 2005-09-11 Release date: 2005-11-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn Biochemistry, 44, 2005
6WTL	Structure of Human pir-miRNA-19b-2 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold 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, POTASSIUM ION, ... Authors: Shoffner, G.M, Peng, Z, Guo, F. Deposit date: 2020-05-03 Release date: 2021-05-05 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Three-dimensional structures of pri-miRNA apical junctions and loops revealed by scaffold-directed crystallography To Be Published
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
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
2GIC	Crystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex Descriptor: 45-MER, Nucleocapsid protein, URANYL (VI) ION Authors: Green, T.J, Zhang, X, Wertz, G.W, Luo, M. Deposit date: 2006-03-28 Release date: 2006-08-22 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.92 Å) Cite: Structure of the vesicular stomatitis virus nucleoprotein-RNA complex unveils how the RNA is sequestered Science, 313, 2006
4Q4Z	Thermus thermophilus RNA polymerase de novo transcription initiation complex Descriptor: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, ADENOSINE-5'-TRIPHOSPHATE, DNA (25-MER), ... Authors: Murakami, K.S. Deposit date: 2014-04-15 Release date: 2014-07-30 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J.Biol.Chem., 289, 2014
4K4U	Poliovirus polymerase elongation complex (r5_form) Descriptor: RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3'), RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)-3'), RNA (5'-R(P*GP*GP*GP*GP*GP*AP*GP*AP*UP*GP*A)-3'), ... Authors: Gong, P, Peersen, O.B. Deposit date: 2013-04-12 Release date: 2013-05-22 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts. Plos One, 8, 2013
1D16	STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS Descriptor: DNA (5'-D(*CP*GP*CP*GP*CP*GP*TP*TP*TP*TP*CP*GP*CP*GP*CP*G)-3') Authors: Chattopadhyaya, R, Grzeskowiak, K, Dickerson, R.E. Deposit date: 1988-04-12 Release date: 1989-01-09 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops. J.Mol.Biol., 211, 1990
6EMS	Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis. Descriptor: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase Authors: Singh, R.K, Versees, W. Deposit date: 2017-10-03 Release date: 2018-06-13 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (1.996 Å) Cite: Structural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism. RNA, 24, 2018
4K4W	Poliovirus polymerase elongation complex (r5+2_form) Descriptor: RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*C)-3'), RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*AP*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3'), RNA-directed RNA polymerase 3D-POL Authors: Gong, P, Peersen, O.B. Deposit date: 2013-04-12 Release date: 2013-05-22 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.69 Å) Cite: Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts. Plos One, 8, 2013
8YGJ	SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt) Descriptor: CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(P*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), DNA (51-MER), ... Authors: Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. Deposit date: 2024-02-26 Release date: 2024-06-05 Last modified: 2024-09-11 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Structural basis for pegRNA-guided reverse transcription by a prime editor. Nature, 631, 2024
4Q5S	Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA Descriptor: ADENOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*CP*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*GP*CP*CP*A)-3'), DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'), ... Authors: Murakami, K.S. Deposit date: 2014-04-17 Release date: 2014-07-09 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (3 Å) Cite: Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J.Biol.Chem., 289, 2014
6UP0	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
8YNP	RNA duplex containing Methylformamide Descriptor: RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHX)P*CP*C)-3') Authors: Kondo, J, Abe, H. Deposit date: 2024-03-11 Release date: 2025-01-22 Method: X-RAY DIFFRACTION (1.4 Å) Cite: Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs. Nucleic Acids Res., 52, 2024
8VFS	oppF ROSE-like RNA thermometer structure Descriptor: RNA (27-MER) Authors: Shaffer, S.N, Passalacqua, L.F.M, Abdelsayed, M.M, Ferre-D'Amare, A.R. Deposit date: 2023-12-21 Release date: 2024-12-25 Last modified: 2025-01-22 Method: X-RAY DIFFRACTION (2.7 Å) Cite: RNA thermometers are widespread upstream of ABC transporter genes in bacteria. J.Biol.Chem., 300, 2024
8YNO	RNA duplex containing Formamide Descriptor: RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHU)P*CP*C)-3'), SPERMINE Authors: Kondo, J, Abe, H. Deposit date: 2024-03-11 Release date: 2024-11-20 Method: X-RAY DIFFRACTION (1.3 Å) Cite: Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs. Nucleic Acids Res., 52, 2024
1FO1	CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE MRNA EXPORT FACTOR TAP Descriptor: NUCLEAR RNA EXPORT FACTOR 1 Authors: Liker, E, Fernandez, E, Izaurralde, E, Conti, E. Deposit date: 2000-08-24 Release date: 2000-11-03 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.9 Å) Cite: The structure of the mRNA export factor TAP reveals a cis arrangement of a non-canonical RNP domain and an LRR domain. EMBO J., 19, 2000
4QBT	Crystal structure of tyrosine bound human tyrosyl tRNA synthetase Descriptor: GLYCEROL, PHOSPHATE ION, POTASSIUM ION, ... Authors: Mathew, S, Schimmel, P. Deposit date: 2014-05-08 Release date: 2014-12-17 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.1 Å) Cite: A human tRNA synthetase is a potent PARP1-activating effector target for resveratrol. Nature, 519, 2014
3ZXI	Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with a tyrosyl-adenylate analog Descriptor: PHOSPHORIC ACID 2-AMINO-3-(4-HYDROXY-PHENYL)-PROPYL ESTER ADENOSIN-5'YL ESTER, TYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL Authors: Bonnefond, L, Frugier, M, Rudinger-Thirion, J, Balg, C, Chenevert, R, Lorber, B, Giege, R, Sauter, C. Deposit date: 2011-08-11 Release date: 2011-11-16 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (2.75 Å) Cite: Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination Cryst.Growth Des., 11, 2011
1L3Z	Crystal Structure Analysis of an RNA Heptamer Descriptor: 5'-R(*GP*UP*AP*UP*AP*CP*A)-3', SODIUM ION Authors: Shi, K, Pan, B, Sundaralingam, M. Deposit date: 2002-03-04 Release date: 2003-02-25 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.01 Å) Cite: The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs Nucleic Acids Res., 31, 2003
4PMI	Crystal structure of Rev and Rev-response-element RNA complex Descriptor: PHOSPHATE ION, Protein Rev, Rev-Response-Element RNA Authors: Jayaraman, B, Crosby, D.C, Homer, C, Ribeiro, I, Mavor, D, Frankel, A.D. Deposit date: 2014-05-21 Release date: 2014-12-24 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.2 Å) Cite: RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. Elife, 4, 2014
4Q93	Crystal structure of resveratrol bound human tyrosyl tRNA synthetase Descriptor: CHLORIDE ION, GLYCEROL, PHOSPHATE ION, ... Authors: Mathew, S, Schimmel, P. Deposit date: 2014-04-28 Release date: 2014-12-17 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.1 Å) Cite: A human tRNA synthetase is a potent PARP1-activating effector target for resveratrol. Nature, 519, 2014
4RMO	Crystal Structure of the CptIN Type III Toxin-Antitoxin System from Eubacterium rectale Descriptor: CALCIUM ION, CptN Toxin, RNA (45-MER) Authors: Rao, F, Voss, J.E, Short, F.L, Luisi, B.F. Deposit date: 2014-10-21 Release date: 2015-09-30 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein-RNA toxin-antitoxin system. Nucleic Acids Res., 43, 2015
1G1X	STRUCTURE OF RIBOSOMAL PROTEINS S15, S6, S18, AND 16S RIBOSOMAL RNA Descriptor: 16S RIBOSOMAL RNA, 30S RIBOSOMAL PROTEIN S15, 30S RIBOSOMAL PROTEIN S18, ... Authors: Agalarov, S.C, Prasad, G.S, Funke, P.M, Stout, C.D, Williamson, J.R. Deposit date: 2000-10-13 Release date: 2000-10-30 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.6 Å) Cite: Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science, 288, 2000

<8687888990919293949596979899100101>