Equivalence class NR_4.0_60810.3 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3PEY|1|B (rep) | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | S. cerevisiae Dbp5 bound to RNA and ADP BeF3 | X-ray diffraction | 1.4 | 2011-03-23 | ||||
| 2 | 3PEW|1|B | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3 | X-ray diffraction | 1.5 | 2011-03-23 | ||||
| 3 | 5ELX|1|B | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | Saccharomyces cerevisiae | Eukarya | S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3 | X-ray diffraction | 1.81 | 2016-02-24 | ||
| 4 | 4ALP|1|E | HEXA URIDINE | synthetic construct | Synthetic | The Lin28b Cold shock domain in complex with hexauridine | X-ray diffraction | 1.48 | 2012-09-05 | ||
| 5 | 2HYI|1|F | 5'-R(*UP*UP*UP*UP*UP*U)-3' | Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA | X-ray diffraction | 2.3 | 2006-08-15 | ||||
| 6 | 2HYI|1|L | 5'-R(*UP*UP*UP*UP*UP*U)-3' | Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA | X-ray diffraction | 2.3 | 2006-08-15 | ||||
| 7 | 3EX7|1|J | RNA (5'-R(*UP*UP*UP*UP*UP*U)-3') | The crystal structure of EJC in its transition state | X-ray diffraction | 2.3 | 2008-12-09 | ||||
| 8 | 3EX7|1|F | RNA (5'-R(*UP*UP*UP*UP*UP*U)-3') | The crystal structure of EJC in its transition state | X-ray diffraction | 2.3 | 2008-12-09 | ||||
| 9 | 3O8C|1|C | RNA (5'-R(P*UP*(5BU)P*UP*UP*UP*U)-3') | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-ray diffraction | 2 | 2011-01-05 | ||||
| 10 | 5BTE|1|D | RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3') | Homo sapiens | Eukarya | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-ray diffraction | 2.4 | 2015-07-22 | ||
| 11 | 3PF5|1|R | hexaribouracil (rU6) | Crystal structure of Bs-CspB in complex with rU6 | X-ray diffraction | 1.68 | 2011-09-21 | ||||
| 12 | 5BTE|1|C | RNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3') | Homo sapiens | Eukarya | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-ray diffraction | 2.4 | 2015-07-22 | ||
| 13 | 3O8R|1|C | RNA (5'-R(P*UP*(5BU)P*UP*UP*UP*U)-3') | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-ray diffraction | 2.3 | 2011-01-05 | ||||
| 14 | 4NL3|1|Z | 5'-R(*UP*UP*UP*UP*UP*U)-3' | Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-ray diffraction | 3.1 | 2014-09-10 | ||||
| 15 | 4Y91|1|O | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | synthetic construct | Synthetic | Crystal Structure of a Thermotoga maritima Hfq homolog | X-ray diffraction | 2.66 | 2016-03-16 | ||
| 16 | 4Y91|1|N | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | synthetic construct | Synthetic | Crystal Structure of a Thermotoga maritima Hfq homolog | X-ray diffraction | 2.66 | 2016-03-16 | ||
| 17 | 4NL3|1|R | 5'-R(*UP*UP*UP*UP*UP*U)-3' | Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-ray diffraction | 3.1 | 2014-09-10 | ||||
| 18 | 1N34|1|Z | A-SITE MESSENGER RNA FRAGMENT | Thermus thermophilus | Bacteria | Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon position | X-ray diffraction | 3.8 | 2002-11-29 | ||
| 19 | 3PF5|1|S | hexaribouracil (rU6) | Crystal structure of Bs-CspB in complex with rU6 | X-ray diffraction | 1.68 | 2011-09-21 | ||||
| 20 | 5SZE|1|C | RNA (5'-R(P*UP*UP*U)-3') | unidentified | Crystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5A | X-ray diffraction | 1.5 | 2017-04-12 | |||
| 21 | 5Z9W|1|R | RNA (6-MER) | synthetic construct | Synthetic | Ebola virus nucleoprotein-RNA complex | Electron microscopy | 3.6 | 2018-10-24 |
Release history
| Release | 9.15 |
|---|---|
| Date | 2018-11-09 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_60810.3 | NR_4.0_60810.2 | 9.15 | (20) 5ELX|1|B, 5BTE|1|D, 5BTE|1|C, 4Y91|1|O, 4Y91|1|N, 4NL3|1|Z, 4NL3|1|R, 4ALP|1|E, 3PF5|1|S, 3PF5|1|R, 3PEY|1|B, 3PEW|1|B, 3O8R|1|C, 3O8C|1|C, 3EX7|1|J, 3EX7|1|F, 2HYI|1|L, 2HYI|1|F, 1N34|1|Z, 5SZE|1|C | (1) 5Z9W|1|R | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_4.0_60810.3 | NR_4.0_60810.4 | 9.16 | (21) 4Y91|1|N, 4NL3|1|Z, 4NL3|1|R, 4ALP|1|E, 3PF5|1|S, 3PF5|1|R, 3PEY|1|B, 3PEW|1|B, 3O8R|1|C, 3O8C|1|C, 5Z9W|1|R, 3EX7|1|J, 5SZE|1|C, 3EX7|1|F, 5ELX|1|B, 2HYI|1|L, 5BTE|1|D, 2HYI|1|F, 5BTE|1|C, 1N34|1|Z, 4Y91|1|O | (0) | (1) 6G2K|1|R |
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 | NAKB_NA_annotation | NAKB_protein_annotation |
|---|---|---|---|---|---|---|---|
| 1 | 4ALP|1|E | Title: The Lin28b Cold shock domain in complex with hexauridine | X-RAY DIFFRACTION | 1.48 | 6 | ||
| 2 | 4Y91|1|O | Title: Crystal Structure of a Thermotoga maritima Hfq homolog | X-RAY DIFFRACTION | 2.66 | 6 | ||
| 3 | 4Y91|1|N | Title: Crystal Structure of a Thermotoga maritima Hfq homolog | X-RAY DIFFRACTION | 2.66 | 6 | ||
| 4 | 4NL3|1|R | Title: Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-RAY DIFFRACTION | 3.1 | 6 | ||
| 5 | 4NL3|1|Z | Title: Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-RAY DIFFRACTION | 3.1 | 6 | ||
| 6 | 3PF5|1|R | Title: Crystal structure of Bs-CspB in complex with rU6 | X-RAY DIFFRACTION | 1.68 | 9 | ||
| 7 | 5BTE|1|D | Title: Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-RAY DIFFRACTION | 2.4 | 4 | ||
| 8 | 5BTE|1|C | Title: Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-RAY DIFFRACTION | 2.4 | 4 | ||
| 9 | 1N34|1|Z | Title: Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon position | X-RAY DIFFRACTION | 3.8 | 4 | ||
| 10 | 3EX7|1|J | Title: The crystal structure of EJC in its transition state | X-RAY DIFFRACTION | 2.3 | 6 | ||
| 11 | 2HYI|1|L | Title: Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA | X-RAY DIFFRACTION | 2.3 | 6 | ||
| 12 | 5ELX|1|B | Title: S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3 | X-RAY DIFFRACTION | 1.81 | 6 | ||
| 13 | 3PEY|1|B | Title: S. cerevisiae Dbp5 bound to RNA and ADP BeF3 | X-RAY DIFFRACTION | 1.4 | 6 | ||
| 14 | 3PEW|1|B | Title: S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3 | X-RAY DIFFRACTION | 1.5 | 6 | ||
| 15 | 3EX7|1|F | Title: The crystal structure of EJC in its transition state | X-RAY DIFFRACTION | 2.3 | 6 | ||
| 16 | 2HYI|1|F | Title: Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA | X-RAY DIFFRACTION | 2.3 | 6 | ||
| 17 | 3PF5|1|S | Title: Crystal structure of Bs-CspB in complex with rU6 | X-RAY DIFFRACTION | 1.68 | 1 | ||
| 18 | 3O8C|1|C | Title: Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-RAY DIFFRACTION | 2 | 5 | ||
| 19 | 3O8R|1|C | Title: Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-RAY DIFFRACTION | 2.3 | 5 | ||
| 20 | 5Z9W|1|R | Title: Ebola virus nucleoprotein-RNA complex | ELECTRON MICROSCOPY | 3.6 | 6 | ||
| 21 | 5SZE|1|C | Title: Crystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5A | X-RAY DIFFRACTION | 1.5 | 3 |
Coloring options: