Equivalence class NR_2.0_94729.9 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4NLF|1|A (rep) | 23S ribosomal RNA Sarcin Ricin Loop | 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL | X-ray diffraction | 1 | 2014-11-19 | ||||
| 2 | 5D99|1|A | RNA (27-MER) hairpin from sarcin-ricin domain of E. coli 23S rRNA | Enterobacteria phage L1 | 3DW4 redetermined by direct methods starting from random phase angles | X-ray diffraction | 0.97 | 2016-04-13 | |||
| 3 | 6Y0Y|1|A | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666U | X-ray diffraction | 0.95 | 2021-02-17 | |||
| 4 | 1Q9A|1|A | Sarcin/ricin 23S rRNA | Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution | X-ray diffraction | 1.04 | 2003-11-25 | ||||
| 5 | 7QP2|1|A | RNA (27-MER) | synthetic construct | 1-deazaguanosine modified-RNA Sarcin Ricin Loop | X-ray diffraction | 0.9 | 2022-07-20 | |||
| 6 | 4NMG|1|A | 23S ribosomal RNA Sarcin Ricin Loop | 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL | X-ray diffraction | 1.01 | 2014-11-19 | ||||
| 7 | 6ZYB|1|A | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | synthetic construct | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | X-ray diffraction | 0.9 | 2020-12-16 | |||
| 8 | 3DW4|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-OCH3 modified | X-ray diffraction | 0.97 | 2009-03-24 | ||||
| 9 | 3DW6|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified | X-ray diffraction | 1 | 2009-03-24 | ||||
| 10 | 7L3R|1|A | RNA (27-MER) | synthetic construct | 23S Sarcin Ricin Loop with a 3-deazapurine A2670 | X-ray diffraction | 1.01 | 2021-05-05 | |||
| 11 | 4Y27|1|A | 27-mer 23S Sarcin-Ricil Loop | Escherichia coli | E.coli 23S Sarcin-Ricil Loop, modified with a 2-Me on G2661 and a methylphosphonate on A2662 | X-ray diffraction | 1 | 2015-11-18 | |||
| 12 | 7JJE|1|A | RNA (27-MER) | synthetic construct | Sarcin-ricin loop with guanosine dithiophosphate residue. | X-ray diffraction | 1.25 | 2020-12-23 | |||
| 13 | 3DVZ|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA | X-ray diffraction | 1 | 2009-03-24 | ||||
| 14 | 4NXH|1|A | 23S ribosomal RNA Sarcin Ricin Loop | Escherichia coli | 2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop | X-ray diffraction | 1.16 | 2014-12-10 | |||
| 15 | 5NQI|1|A | E.Coli 27-mer SRL RNA | Escherichia coli | E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification | X-ray diffraction | 0.85 | 2017-07-26 | |||
| 16 | 3S7C|1|A | Ecoli 23 S rRNA Sarcin Ricin loop | Crystal structure of a 2'-azido-uridine-modified RNA | X-ray diffraction | 1.1 | 2012-04-11 | ||||
| 17 | 5MRX|1|A | RNA (27-MER) | Escherichia coli | 27-nt SRL with a 5-hydroxymethyl cytidine modification | X-ray diffraction | 0.85 | 2018-01-17 | |||
| 18 | 3DW5|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23S rRNA, U2656-OCH3 modified | X-ray diffraction | 0.96 | 2009-03-24 | ||||
| 19 | 3DW7|1|A | Sarcin/Ricin Domain from E. Coli 23 S rRNA | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2656-SeCH3 modified | X-ray diffraction | 1 | 2009-03-24 | ||||
| 20 | 483D|1|A | SARCIN/RICIN RRNA DOMAIN | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-ray diffraction | 1.11 | 1999-10-08 | ||||
| 21 | 3S8U|1|A | Ecoli 23 S rRNA Sarcin Ricin loop | Escherichia coli | Crystal structure of a 2-azido-adenine-modified RNA | X-ray diffraction | 1.2 | 2012-04-11 | |||
| 22 | 7JJD|1|A | RNA (27-MER) | synthetic construct | Sarcin-ricin loop with guanosine monothiophosphate residue. | X-ray diffraction | 1.21 | 2020-12-23 | |||
| 23 | 1MSY|1|A | SARCIN/RICIN DOMAIN FROM 23 S RRNA | GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA | X-ray diffraction | 1.41 | 2003-02-25 | ||||
| 24 | 480D|1|A | SARCIN/RICIN DOMAIN FROM 23 S RRNA | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-ray diffraction | 1.5 | 1999-10-08 | ||||
| 25 | 6Y0T|1|B | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-ray diffraction | 1.393 | 2021-02-17 | |||
| 26 | 6Y0T|1|A | RNA (27-MER) | synthetic construct | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-ray diffraction | 1.393 | 2021-02-17 | |||
| 27 | 7JJF|1|A | RNA/DNA (27-mer) | Escherichia coli | Sarcin-ricin loop with modified residue. | X-ray diffraction | 1.2 | 2020-12-23 | |||
| 28 | 7EEN|1|A | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 1.7 | 2022-03-23 | |||
| 29 | 7EEN|1|B | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 1.7 | 2022-03-23 | |||
| 30 | 7EEN|1|D | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 1.7 | 2022-03-23 | |||
| 31 | 1JBS|1|D | 29-mer sarcin/ricin domain RNA analog | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-ray diffraction | 1.97 | 2001-10-26 | ||||
| 32 | 7EEN|1|C | DNA/RNA (27-MER) | synthetic construct | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-ray diffraction | 1.7 | 2022-03-23 | |||
| 33 | 1JBS|1|C | 29-mer sarcin/ricin domain RNA analog | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-ray diffraction | 1.97 | 2001-10-26 | ||||
| 34 | 7UCR|1|A | Sarcin-Ricin loop RNA | Homo sapiens | Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA | X-ray diffraction | 1 | 2022-07-20 |
Release history
| Release | 3.240 | 3.241 | 3.242 | 3.243 | 3.244 | 3.245 | 3.246 | 3.247 | 3.248 | 3.249 | 3.250 | 3.251 | 3.252 | 3.253 | 3.254 | 3.255 | 3.256 | 3.257 | 3.258 | 3.259 | 3.260 | 3.261 | 3.262 | 3.263 | 3.264 | 3.265 | 3.266 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2022-07-20 | 2022-07-27 | 2022-08-03 | 2022-08-10 | 2022-08-17 | 2022-08-24 | 2022-08-31 | 2022-09-07 | 2022-09-14 | 2022-09-21 | 2022-09-28 | 2022-10-05 | 2022-10-12 | 2022-10-19 | 2022-10-26 | 2022-11-02 | 2022-11-09 | 2022-11-16 | 2022-11-23 | 2022-11-30 | 2022-12-07 | 2022-12-14 | 2022-12-21 | 2022-12-28 | 2023-01-04 | 2023-01-11 | 2023-01-18 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.0_94729.9 | NR_2.0_94729.8 | 3.240 | (32) 3DW6|1|A, 6ZYB|1|A, 3DW5|1|A, 6Y0Y|1|A, 3DW4|1|A, 6Y0T|1|B, 3DVZ|1|A, 6Y0T|1|A, 1Q9A|1|A, 5NQI|1|A, 1MSY|1|A, 5MRX|1|A, 1JBS|1|D, 5D99|1|A, 1JBS|1|C, 4Y27|1|A, 4NXH|1|A, 7L3R|1|A, 4NMG|1|A, 7JJF|1|A, 4NLF|1|A, 7JJE|1|A, 483D|1|A, 7JJD|1|A, 480D|1|A, 7EEN|1|D, 3S8U|1|A, 7EEN|1|C, 3S7C|1|A, 7EEN|1|B, 3DW7|1|A, 7EEN|1|A | (2) 7QP2|1|A, 7UCR|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.0_94729.9 | NR_2.0_94729.10 | 3.267 | (34) 3DW7|1|A, 7EEN|1|A, 3DW6|1|A, 6ZYB|1|A, 3DW5|1|A, 6Y0Y|1|A, 3DW4|1|A, 6Y0T|1|B, 3DVZ|1|A, 6Y0T|1|A, 1Q9A|1|A, 5NQI|1|A, 1MSY|1|A, 5MRX|1|A, 1JBS|1|D, 5D99|1|A, 7UCR|1|A, 1JBS|1|C, 4Y27|1|A, 7QP2|1|A, 4NXH|1|A, 7L3R|1|A, 4NMG|1|A, 7JJF|1|A, 4NLF|1|A, 7JJE|1|A, 483D|1|A, 7JJD|1|A, 480D|1|A, 7EEN|1|D, 3S8U|1|A, 7EEN|1|C, 3S7C|1|A, 7EEN|1|B | (0) | (1) 7QSH|1|A |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 1MSY|1|A | GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA | X-RAY DIFFRACTION | 1.41 | 31 |
| 2 | 6Y0Y|1|A | Sarcin Ricin Loop, mutant C2666U | X-RAY DIFFRACTION | 0.95 | 27 |
| 3 | 6Y0T|1|A | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-RAY DIFFRACTION | 1.393 | 30 |
| 4 | 6Y0T|1|B | Sarcin Ricin Loop, mutant C2666A U2653G C2667A | X-RAY DIFFRACTION | 1.393 | 30 |
| 5 | 4NLF|1|A | 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL | X-RAY DIFFRACTION | 1 | 28 |
| 6 | 4NMG|1|A | 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL | X-RAY DIFFRACTION | 1.01 | 36 |
| 7 | 3DW7|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2656-SeCH3 modified | X-RAY DIFFRACTION | 1 | 37 |
| 8 | 3S7C|1|A | Crystal structure of a 2'-azido-uridine-modified RNA | X-RAY DIFFRACTION | 1.1 | 32 |
| 9 | 3DW6|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified | X-RAY DIFFRACTION | 1 | 28 |
| 10 | 3DW4|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-OCH3 modified | X-RAY DIFFRACTION | 0.97 | 26 |
| 11 | 5D99|1|A | 3DW4 redetermined by direct methods starting from random phase angles | X-RAY DIFFRACTION | 0.97 | 30 |
| 12 | 4NXH|1|A | 2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop | X-RAY DIFFRACTION | 1.16 | 32 |
| 13 | 6ZYB|1|A | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | X-RAY DIFFRACTION | 0.9 | 30 |
| 14 | 7JJE|1|A | Sarcin-ricin loop with guanosine dithiophosphate residue. | X-RAY DIFFRACTION | 1.25 | 29 |
| 15 | 3DVZ|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA | X-RAY DIFFRACTION | 1 | 35 |
| 16 | 7JJD|1|A | Sarcin-ricin loop with guanosine monothiophosphate residue. | X-RAY DIFFRACTION | 1.21 | 29 |
| 17 | 3S8U|1|A | Crystal structure of a 2-azido-adenine-modified RNA | X-RAY DIFFRACTION | 1.2 | 34 |
| 18 | 7L3R|1|A | 23S Sarcin Ricin Loop with a 3-deazapurine A2670 | X-RAY DIFFRACTION | 1.01 | 30 |
| 19 | 3DW5|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23S rRNA, U2656-OCH3 modified | X-RAY DIFFRACTION | 0.96 | 32 |
| 20 | 7UCR|1|A | Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA | X-RAY DIFFRACTION | 1 | 56 |
| 21 | 7QP2|1|A | 1-deazaguanosine modified-RNA Sarcin Ricin Loop | X-RAY DIFFRACTION | 0.9 | 32 |
| 22 | 1Q9A|1|A | Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution | X-RAY DIFFRACTION | 1.04 | 38 |
| 23 | 483D|1|A | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-RAY DIFFRACTION | 1.11 | 39 |
| 24 | 5NQI|1|A | E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification | X-RAY DIFFRACTION | 0.85 | 34 |
| 25 | 5MRX|1|A | 27-nt SRL with a 5-hydroxymethyl cytidine modification | X-RAY DIFFRACTION | 0.85 | 34 |
| 26 | 7JJF|1|A | Sarcin-ricin loop with modified residue. | X-RAY DIFFRACTION | 1.2 | 27 |
| 27 | 4Y27|1|A | E.coli 23S Sarcin-Ricil Loop, modified with a 2-Me on G2661 and a methylphosphonate on A2662 | X-RAY DIFFRACTION | 1 | 25 |
| 28 | 480D|1|A | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-RAY DIFFRACTION | 1.5 | 27 |
| 29 | 7EEN|1|A | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 14 |
| 30 | 7EEN|1|B | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 15 |
| 31 | 7EEN|1|C | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 14 |
| 32 | 7EEN|1|D | Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA | X-RAY DIFFRACTION | 1.7 | 14 |
| 33 | 1JBS|1|D | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-RAY DIFFRACTION | 1.97 | 17 |
| 34 | 1JBS|1|C | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-RAY DIFFRACTION | 1.97 | 17 |