Equivalence class NR_20.0_94729.5 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 | 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 | ||||
| 4 | 4NMG|1|A | 23S ribosomal RNA Sarcin Ricin Loop | 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL | X-ray diffraction | 1.01 | 2014-11-19 | ||||
| 5 | 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 | |||
| 6 | 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 | ||||
| 7 | 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 | ||||
| 8 | 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 | |||
| 9 | 7JJE|1|A | RNA (27-MER) | synthetic construct | Sarcin-ricin loop with guanosine dithiophosphate residue. | X-ray diffraction | 1.25 | 2020-12-23 | |||
| 10 | 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 | ||||
| 11 | 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 | |||
| 12 | 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 | |||
| 13 | 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 | ||||
| 14 | 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 | |||
| 15 | 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 | ||||
| 16 | 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 | ||||
| 17 | 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 | ||||
| 18 | 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 | |||
| 19 | 7JJD|1|A | RNA (27-MER) | synthetic construct | Sarcin-ricin loop with guanosine monothiophosphate residue. | X-ray diffraction | 1.21 | 2020-12-23 | |||
| 20 | 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 | ||||
| 21 | 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 | ||||
| 22 | 7JJF|1|A | RNA/DNA (27-mer) | Escherichia coli | Sarcin-ricin loop with modified residue. | X-ray diffraction | 1.2 | 2020-12-23 | |||
| 23 | 1JBR|1|D | 31-mer SRD RNA analog | Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor | X-ray diffraction | 2.15 | 2001-10-26 | ||||
| 24 | 1JBT|1|C | 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | X-ray diffraction | 2.7 | 2001-10-26 | ||||
| 25 | 6ZXZ|1|B | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | synthetic construct | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-ray diffraction | 2.44 | 2020-12-16 | |||
| 26 | 1JBT|1|D | 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | X-ray diffraction | 2.7 | 2001-10-26 | ||||
| 27 | 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 | ||||
| 28 | 6ZXZ|1|A | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | synthetic construct | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-ray diffraction | 2.44 | 2020-12-16 | |||
| 29 | 6ZXZ|1|C | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | synthetic construct | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-ray diffraction | 2.44 | 2020-12-16 | |||
| 30 | 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 | ||||
| 31 | 3EP2|1|D | Fragment H95 of the 23S rRNA | Escherichia coli | Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM | Electron microscopy | 9 | 2008-12-16 | |||
| 32 | 3EQ3|1|D | Fragment H95 of the 23S rRNA | Escherichia coli | Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM | Electron microscopy | 9 | 2008-12-16 | |||
| 33 | 3DEG|1|I | 50S RNA helix 95 | Escherichia coli | Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP | Electron microscopy | 10.9 | 2008-08-19 | |||
| 34 | 1EG0|1|M | HELIX 95 OF 23S RRNA | Escherichia coli | FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME | Electron microscopy | 11.5 | 2000-03-06 | |||
| 35 | 3EQ4|1|D | Fragment H95 of the 23S rRNA | Escherichia coli | Model of tRNA(Leu)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM | Electron microscopy | 12 | 2008-12-16 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_20.0_94729.5 | NR_20.0_94729.4 | 3.158 | (32) 483D|1|A, 6ZXZ|1|C, 3DVZ|1|A, 480D|1|A, 3DEG|1|I, 6ZXZ|1|B, 3S8U|1|A, 1Q9A|1|A, 6ZXZ|1|A, 3S7C|1|A, 1MSY|1|A, 5NQI|1|A, 3EQ4|1|D, 1JBT|1|D, 5MRX|1|A, 3EQ3|1|D, 1JBT|1|C, 5D99|1|A, 3EP2|1|D, 1JBS|1|D, 4Y27|1|A, 3DW7|1|A, 1JBS|1|C, 4NXH|1|A, 3DW6|1|A, 1JBR|1|D, 4NMG|1|A, 3DW5|1|A, 1EG0|1|M, 4NLF|1|A, 3DW4|1|A, 6ZYB|1|A | (3) 7JJD|1|A, 7JJF|1|A, 7JJE|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_20.0_94729.5 | NR_20.0_94729.6 | 3.166 | (35) 7JJE|1|A, 1Q9A|1|A, 3DW6|1|A, 3S7C|1|A, 4NXH|1|A, 6ZXZ|1|A, 1JBR|1|D, 1MSY|1|A, 4NMG|1|A, 3DW5|1|A, 5NQI|1|A, 7JJD|1|A, 3EQ4|1|D, 1EG0|1|M, 1JBT|1|D, 4NLF|1|A, 3DW4|1|A, 5MRX|1|A, 3EQ3|1|D, 6ZYB|1|A, 1JBT|1|C, 483D|1|A, 3DVZ|1|A, 5D99|1|A, 3EP2|1|D, 6ZXZ|1|C, 1JBS|1|D, 480D|1|A, 3DEG|1|I, 4Y27|1|A, 3DW7|1|A, 6ZXZ|1|B, 7JJF|1|A, 3S8U|1|A, 1JBS|1|C | (0) | (3) 6Y0Y|1|A, 6Y0T|1|A, 6Y0T|1|B |
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 | 4NLF|1|A | 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL | X-RAY DIFFRACTION | 1 | 28 |
| 3 | 480D|1|A | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-RAY DIFFRACTION | 1.5 | 27 |
| 4 | 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 |
| 5 | 5NQI|1|A | E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification | X-RAY DIFFRACTION | 0.85 | 34 |
| 6 | 5MRX|1|A | 27-nt SRL with a 5-hydroxymethyl cytidine modification | X-RAY DIFFRACTION | 0.85 | 34 |
| 7 | 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 |
| 8 | 483D|1|A | CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA | X-RAY DIFFRACTION | 1.11 | 39 |
| 9 | 7JJF|1|A | Sarcin-ricin loop with modified residue. | X-RAY DIFFRACTION | 1.2 | 27 |
| 10 | 4NXH|1|A | 2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop | X-RAY DIFFRACTION | 1.16 | 32 |
| 11 | 6ZYB|1|A | Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification | X-RAY DIFFRACTION | 0.9 | 30 |
| 12 | 7JJE|1|A | Sarcin-ricin loop with guanosine dithiophosphate residue. | X-RAY DIFFRACTION | 1.25 | 29 |
| 13 | 3DVZ|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA | X-RAY DIFFRACTION | 1 | 35 |
| 14 | 7JJD|1|A | Sarcin-ricin loop with guanosine monothiophosphate residue. | X-RAY DIFFRACTION | 1.21 | 29 |
| 15 | 3S8U|1|A | Crystal structure of a 2-azido-adenine-modified RNA | X-RAY DIFFRACTION | 1.2 | 34 |
| 16 | 3DW5|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23S rRNA, U2656-OCH3 modified | X-RAY DIFFRACTION | 0.96 | 32 |
| 17 | 4NMG|1|A | 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL | X-RAY DIFFRACTION | 1.01 | 36 |
| 18 | 3DW7|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2656-SeCH3 modified | X-RAY DIFFRACTION | 1 | 37 |
| 19 | 5D99|1|A | 3DW4 redetermined by direct methods starting from random phase angles | X-RAY DIFFRACTION | 0.97 | 30 |
| 20 | 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 |
| 21 | 3DW6|1|A | Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified | X-RAY DIFFRACTION | 1 | 28 |
| 22 | 3S7C|1|A | Crystal structure of a 2'-azido-uridine-modified RNA | X-RAY DIFFRACTION | 1.1 | 32 |
| 23 | 6ZXZ|1|A | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 25 |
| 24 | 6ZXZ|1|C | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 25 |
| 25 | 6ZXZ|1|B | Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification | X-RAY DIFFRACTION | 2.44 | 25 |
| 26 | 3DEG|1|I | Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP | ELECTRON MICROSCOPY | 10.9 | 29 |
| 27 | 1JBR|1|D | Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor | X-RAY DIFFRACTION | 2.15 | 31 |
| 28 | 1JBT|1|D | CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | X-RAY DIFFRACTION | 2.7 | 29 |
| 29 | 1JBT|1|C | CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG | X-RAY DIFFRACTION | 2.7 | 29 |
| 30 | 1JBS|1|D | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-RAY DIFFRACTION | 1.97 | 17 |
| 31 | 1JBS|1|C | Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog | X-RAY DIFFRACTION | 1.97 | 17 |
| 32 | 3EQ4|1|D | Model of tRNA(Leu)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM | ELECTRON MICROSCOPY | 12 | 28 |
| 33 | 1EG0|1|M | FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME | ELECTRON MICROSCOPY | 11.5 | 26 |
| 34 | 3EP2|1|D | Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM | ELECTRON MICROSCOPY | 9 | 28 |
| 35 | 3EQ3|1|D | Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM | ELECTRON MICROSCOPY | 9 | 28 |