Equivalence class NR_3.5_74924.9 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 | 6G2K|1|R | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | synthetic construct | Synthetic | Structure of HuR RRM3 in complex with RNA (UUUUUU) | X-ray diffraction | 2.01 | 2018-10-31 | ||
| 7 | 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 | ||||
| 8 | 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 | ||||
| 9 | 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 | |||
| 10 | 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 | ||||
| 11 | 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 | ||||
| 12 | 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 | ||
| 13 | 3PF5|1|R | hexaribouracil (rU6) | Crystal structure of Bs-CspB in complex with rU6 | X-ray diffraction | 1.68 | 2011-09-21 | ||||
| 14 | 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 | ||
| 15 | 6I0U|1|B | RNA (5'-R(*UP*UP*UP*U)-3') | Drosophila melanogaster | Eukarya | Crystal structure of DmTailor in complex with U6 RNA | X-ray diffraction | 2 | 2018-12-05 | ||
| 16 | 5ZSA|1|C | RNA (5'-R(P*UP*UP*UP*U)-3') | synthetic construct | Synthetic | Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU | X-ray diffraction | 2.5 | 2019-01-30 | ||
| 17 | 5ZSA|1|D | RNA (5'-R(P*UP*UP*UP*U)-3') | synthetic construct | Synthetic | Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU | X-ray diffraction | 2.5 | 2019-01-30 | ||
| 18 | 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 | ||||
| 19 | 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 | ||||
| 20 | 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 | ||
| 21 | 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 | ||
| 22 | 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 | ||||
| 23 | 3PF5|1|S | hexaribouracil (rU6) | Crystal structure of Bs-CspB in complex with rU6 | X-ray diffraction | 1.68 | 2011-09-21 |
Release history
| Release | 3.86 | 3.87 | 3.88 | 3.89 | 3.90 | 3.91 | 3.92 | 3.93 | 3.94 | 3.95 | 3.96 | 3.97 | 3.98 | 3.99 | 3.100 | 3.101 | 3.102 | 3.103 | 3.104 | 3.105 | 3.106 | 3.107 | 3.108 | 3.109 | 3.110 | 3.111 | 3.112 | 3.113 | 3.114 | 3.115 | 3.116 | 3.117 | 3.118 | 3.119 | 3.120 | 3.121 | 3.122 | 3.123 | 3.124 | 3.125 | 3.126 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2019-08-09 | 2019-08-16 | 2019-08-23 | 2019-08-28 | 2019-09-04 | 2019-09-11 | 2019-09-19 | 2019-09-25 | 2019-10-03 | 2019-10-09 | 2019-10-16 | 2019-10-23 | 2019-10-30 | 2019-11-06 | 2019-11-13 | 2019-11-20 | 2019-11-27 | 2019-12-04 | 2019-12-11 | 2019-12-18 | 2019-12-25 | 2020-01-01 | 2020-01-08 | 2020-01-15 | 2020-01-22 | 2020-01-29 | 2020-02-05 | 2020-02-12 | 2020-02-19 | 2020-02-26 | 2020-03-04 | 2020-03-11 | 2020-03-18 | 2020-03-25 | 2020-04-01 | 2020-04-08 | 2020-04-15 | 2020-04-22 | 2020-04-29 | 2020-05-06 | 2020-05-13 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_74924.9 | NR_3.5_74924.8 | 3.86 | (23) 2HYI|1|F, 4Y91|1|N, 4Y91|1|O, 5BTE|1|C, 5BTE|1|D, 5ELX|1|B, 5SZE|1|C, 5ZSA|1|C, 5ZSA|1|D, 6G2K|1|R, 4NL3|1|Z, 4NL3|1|R, 4ALP|1|E, 2HYI|1|L, 3EX7|1|F, 3EX7|1|J, 3O8C|1|C, 3O8R|1|C, 3PEW|1|B, 3PEY|1|B, 3PF5|1|R, 3PF5|1|S, 6I0U|1|B | (0) | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_74924.9 | NR_3.5_74924.10 | 3.127 | (23) 6G2K|1|R, 3O8R|1|C, 5ZSA|1|D, 3O8C|1|C, 5ZSA|1|C, 3EX7|1|J, 5SZE|1|C, 3EX7|1|F, 5ELX|1|B, 2HYI|1|L, 5BTE|1|D, 2HYI|1|F, 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, 6I0U|1|B, 3PEW|1|B | (0) | (1) 6WRE|1|D |
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 | 5SZE|1|C | Crystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5A | X-RAY DIFFRACTION | 1.5 | 3 |
| 2 | 4ALP|1|E | The Lin28b Cold shock domain in complex with hexauridine | X-RAY DIFFRACTION | 1.48 | 6 |
| 3 | 5ZSA|1|C | Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU | X-RAY DIFFRACTION | 2.5 | 4 |
| 4 | 5ZSA|1|D | Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU | X-RAY DIFFRACTION | 2.5 | 4 |
| 5 | 4NL3|1|R | Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-RAY DIFFRACTION | 3.1 | 6 |
| 6 | 4Y91|1|O | Crystal Structure of a Thermotoga maritima Hfq homolog | X-RAY DIFFRACTION | 2.66 | 6 |
| 7 | 4Y91|1|N | Crystal Structure of a Thermotoga maritima Hfq homolog | X-RAY DIFFRACTION | 2.66 | 6 |
| 8 | 4NL3|1|Z | Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-RAY DIFFRACTION | 3.1 | 6 |
| 9 | 3PF5|1|S | Crystal structure of Bs-CspB in complex with rU6 | X-RAY DIFFRACTION | 1.68 | 1 |
| 10 | 3O8C|1|C | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-RAY DIFFRACTION | 2 | 5 |
| 11 | 3PEW|1|B | S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3 | X-RAY DIFFRACTION | 1.5 | 6 |
| 12 | 5ELX|1|B | S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3 | X-RAY DIFFRACTION | 1.81 | 6 |
| 13 | 3PEY|1|B | S. cerevisiae Dbp5 bound to RNA and ADP BeF3 | X-RAY DIFFRACTION | 1.4 | 6 |
| 14 | 3EX7|1|F | The crystal structure of EJC in its transition state | X-RAY DIFFRACTION | 2.3 | 6 |
| 15 | 3EX7|1|J | The crystal structure of EJC in its transition state | X-RAY DIFFRACTION | 2.3 | 6 |
| 16 | 2HYI|1|F | Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA | X-RAY DIFFRACTION | 2.3 | 6 |
| 17 | 2HYI|1|L | Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA | X-RAY DIFFRACTION | 2.3 | 6 |
| 18 | 5BTE|1|D | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-RAY DIFFRACTION | 2.4 | 4 |
| 19 | 5BTE|1|C | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-RAY DIFFRACTION | 2.4 | 4 |
| 20 | 3PF5|1|R | Crystal structure of Bs-CspB in complex with rU6 | X-RAY DIFFRACTION | 1.68 | 9 |
| 21 | 3O8R|1|C | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-RAY DIFFRACTION | 2.3 | 5 |
| 22 | 6I0U|1|B | Crystal structure of DmTailor in complex with U6 RNA | X-RAY DIFFRACTION | 2 | 4 |
| 23 | 6G2K|1|R | Structure of HuR RRM3 in complex with RNA (UUUUUU) | X-RAY DIFFRACTION | 2.01 | 6 |