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8HIO	Cryo-EM structure of the Cas12m2-crRNA binary complex Descriptor: Cas12m2, MAGNESIUM ION, RNA (56-MER), ... Authors: Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. Deposit date: 2022-11-21 Release date: 2023-04-12 Last modified: 2023-08-30 Method: ELECTRON MICROSCOPY (3.73 Å) Cite: Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme. Nat.Struct.Mol.Biol., 30, 2023
8HHM	Cryo-EM structure of the Cas12m2-crRNA-target DNA ternary complex intermediate state Descriptor: Cas12m2, DNA (36-MER), MAGNESIUM ION, ... Authors: Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. Deposit date: 2022-11-16 Release date: 2023-04-12 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (3.08 Å) Cite: Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme. Nat.Struct.Mol.Biol., 30, 2023
5F9H	Crystal structure of RIG-I helicase-RD in complex with 24-mer 5' triphosphate hairpin RNA Descriptor: GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Probable ATP-dependent RNA helicase DDX58, ... Authors: Wang, C, Marcotrigiano, J, Miller, M, Jiang, F. Deposit date: 2015-12-09 Release date: 2016-01-13 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.1 Å) Cite: Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc.Natl.Acad.Sci.USA, 113, 2016
8I43	Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of base pairs 3' adjacent to the bulge out residues Descriptor: 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide, RNA-C-3GC-uucg Authors: Ichijo, R, Kamimura, T, Kawai, G. Deposit date: 2023-01-18 Release date: 2023-03-29 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3' adjacent to the bulged residues. Front Mol Biosci, 10, 2023
8I44	Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of base pairs 3' adjacent to the bulge out residues Descriptor: 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide, RNA-C-3AU-uucg Authors: Ichijo, R, Kamimura, T, Kawai, G. Deposit date: 2023-01-18 Release date: 2023-03-29 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3' adjacent to the bulged residues. Front Mol Biosci, 10, 2023
8I45	Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of base pairs 3' adjacent to the bulge out residues Descriptor: 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide, RNA-G-3GC-uucg Authors: Ichijo, R, Kamimura, T, Kawai, G. Deposit date: 2023-01-18 Release date: 2023-03-29 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3' adjacent to the bulged residues. Front Mol Biosci, 10, 2023
8I46	Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of base pairs 3' adjacent to the bulge out residues Descriptor: 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide, RNA-G-3AU-uucg Authors: Ichijo, R, Kamimura, T, Kawai, G. Deposit date: 2023-01-18 Release date: 2023-03-29 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3' adjacent to the bulged residues. Front Mol Biosci, 10, 2023
8TNS	Solution structure of poly(UG) RNA (GU)12 G-quadruplex Descriptor: RNA (5'-R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*U)-3') Authors: Escobar, C.A, Petersen, R, Butcher, S.E. Deposit date: 2023-08-02 Release date: 2023-11-15 Last modified: 2024-05-15 Method: SOLUTION NMR, SOLUTION SCATTERING Cite: Solution Structure of Poly(UG) RNA. J.Mol.Biol., 435, 2023
7TQV	SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA Descriptor: RNA (33-MER), Uridylate-specific endoribonuclease Authors: Frazier, M.N, Krahn, J.M, Butay, K.J, Dillard, L.B, Borgnia, M.J, Stanley, R.E. Deposit date: 2022-01-27 Release date: 2022-03-23 Last modified: 2024-06-12 Method: ELECTRON MICROSCOPY (3.43 Å) Cite: Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease. Nucleic Acids Res., 50, 2022
7TJ2	SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA Descriptor: RNA (31-MER), Uridylate-specific endoribonuclease nsp15 Authors: Frazier, M.N, Krahn, J.M, Butay, K.J, Dillard, L.B, Borgnia, M.J, Stanley, R.E. Deposit date: 2022-01-14 Release date: 2022-03-23 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease. Nucleic Acids Res., 50, 2022
6I1W	Structure of the RNA duplex containing pseudouridine residue (5'-Gp(PSU)pC-3' sequence context) Descriptor: RNA (5'-R(*AP*CP*UP*GP*AP*CP*UP*GP*A)-3'), RNA (5'-R(*UP*CP*AP*GP*(PSU)P*CP*AP*GP*U)-3') Authors: Deb, I, Popenda, L, Sarzynska, J, Gdaniec, Z. Deposit date: 2018-10-30 Release date: 2019-11-20 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair. Sci Rep, 9, 2019
6I1V	Structure of the RNA duplex containing pseudouridine residue (5'-Cp(PSU)pG-3' sequence context) Descriptor: RNA (5'-R(*AP*CP*UP*CP*AP*GP*UP*GP*A)-3'), RNA (5'-R(*UP*CP*AP*CP*(PSU)P*GP*AP*GP*U)-3') Authors: Deb, I, Popenda, L, Sarzynska, J, Gdaniec, Z. Deposit date: 2018-10-30 Release date: 2019-11-20 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair. Sci Rep, 9, 2019
1PUD	TRNA-GUANINE TRANSGLYCOSYLASE Descriptor: TRNA-GUANINE TRANSGLYCOSYLASE, ZINC ION Authors: Romier, C, Reuter, K, Suck, D, Ficner, R. Deposit date: 1996-06-28 Release date: 1997-07-07 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (1.85 Å) Cite: Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. EMBO J., 15, 1996
6PIG	V. cholerae TniQ-Cascade complex, closed conformation Descriptor: RNA (60-MER), TniQ monomer 1, TniQ monomer 2, ... Authors: Halpin-Healy, T, Klompe, S, Sternberg, S.H. Deposit date: 2019-06-26 Release date: 2019-10-02 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (3.5 Å) Cite: Structural basis of DNA targeting by a transposon-encoded CRISPR-Cas system. Nature, 577, 2020
8DMB	Structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with omega RNA and target DNA Descriptor: MAGNESIUM ION, Ubiquitin-like protein SMT3,IsrB protein,monomeric superfolder Green Fluorescent Protein, non-target DNA, ... Authors: Seiichi, H, Kappel, K, Zhang, F. Deposit date: 2022-07-08 Release date: 2022-10-19 Last modified: 2024-06-12 Method: ELECTRON MICROSCOPY (3.1 Å) Cite: Structure of the OMEGA nickase IsrB in complex with omega RNA and target DNA. Nature, 610, 2022
1PXG	Crystal structure of the mutated tRNA-guanine transglycosylase (TGT) D280E complexed with preQ1 Descriptor: 7-DEAZA-7-AMINOMETHYL-GUANINE, GLYCEROL, Queuine tRNA-ribosyltransferase, ... Authors: Kittendorf, J.D, Sgraja, T, Reuter, K, Klebe, G, Garcia, G.A. Deposit date: 2003-07-04 Release date: 2003-09-09 Last modified: 2023-08-16 Method: X-RAY DIFFRACTION (1.7 Å) Cite: An essential role for aspartate 264 in catalysis by tRNA-guanine transglycosylase from Escherichia coli. J.Biol.Chem., 278, 2003
3TP2	Crystal Structure of the Splicing Factor Cwc2 from yeast Descriptor: Pre-mRNA-splicing factor CWC2, SODIUM ION, ZINC ION Authors: Schmitzova, J. Deposit date: 2011-09-07 Release date: 2012-03-14 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Crystal structure of Cwc2 reveals a novel architecture of a multipartite RNA-binding protein. Embo J., 31, 2012
1OXJ	Crystal structure of the Smaug RNA binding domain Descriptor: RNA-binding protein Smaug Authors: Green, J.B, Gardner, C.D, Wharton, R.P, Aggarwal, A.K. Deposit date: 2003-04-02 Release date: 2003-07-08 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (1.8 Å) Cite: RNA recognition via the SAM domain of Smaug. Mol.Cell, 11, 2003
8HHL	Cryo-EM structure of the Cas12m2-crRNA-target DNA full R-loop complex Descriptor: Cas12m2, MAGNESIUM ION, NTS (36-MER), ... Authors: Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. Deposit date: 2022-11-16 Release date: 2023-04-12 Last modified: 2023-08-30 Method: ELECTRON MICROSCOPY (2.87 Å) Cite: Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme. Nat.Struct.Mol.Biol., 30, 2023
6OV0	Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 Descriptor: RNA (5'-R(*AP*AP*AP*(A23))-3'), Uncharacterized protein Authors: Jia, N, Patel, D.J. Deposit date: 2019-05-06 Release date: 2019-07-31 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.8 Å) Cite: CRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA4Cleavage with ApA>p Formation Terminating RNase Activity. Mol.Cell, 75, 2019
7TDB	Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, manganese ions Descriptor: MAGNESIUM ION, MANGANESE (II) ION, [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic acid, ... Authors: Nuthanakanti, A, Serganov, A. Deposit date: 2021-12-30 Release date: 2022-02-16 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.56 Å) Cite: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. Acs Chem.Biol., 17, 2022
7TD7	Crystal structure of an E. coli thiM riboswitch bound to thiamine, manganese ions Descriptor: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM, MAGNESIUM ION, MANGANESE (II) ION, ... Authors: Nuthanakanti, A, Serganov, A. Deposit date: 2021-12-30 Release date: 2022-02-16 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.95 Å) Cite: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. Acs Chem.Biol., 17, 2022
7TDC	Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, calcium ions Descriptor: CALCIUM ION, MAGNESIUM ION, [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic acid, ... Authors: Nuthanakanti, A, Serganov, A. Deposit date: 2021-12-30 Release date: 2022-02-16 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.46 Å) Cite: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. Acs Chem.Biol., 17, 2022
7TDA	Crystal structure of the E. coli thiM riboswitch in complex with thiamine pyrophosphate, manganese ions Descriptor: MAGNESIUM ION, MANGANESE (II) ION, THIAMINE DIPHOSPHATE, ... Authors: Nuthanakanti, A, Serganov, A. Deposit date: 2021-12-30 Release date: 2022-02-16 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.25 Å) Cite: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. Acs Chem.Biol., 17, 2022
7V94	Cryo-EM structure of the Cas12c2-sgRNA-target DNA ternary complex Descriptor: Cas12c2, sgRNA, target DNA (non target strand), ... Authors: Kurihara, N, Hirano, H, Tomita, A, Kobayashi, K, Kusakizako, T, Nishizawa, T, Yamashita, K, Nishimasu, H, Nureki, O. Deposit date: 2021-08-24 Release date: 2022-04-13 Last modified: 2024-06-12 Method: ELECTRON MICROSCOPY (2.7 Å) Cite: Structure of the type V-C CRISPR-Cas effector enzyme. Mol.Cell, 82, 2022

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