Equivalence class NR_4.0_74924.16 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 | 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 | 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 | 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 | 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 | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-ray diffraction | 2.4 | 2015-07-22 | |||
| 15 | 6WRE|1|D | RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3') | Homo sapiens | Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion | X-ray diffraction | 2 | 2020-05-13 | |||
| 16 | 6I0U|1|B | RNA (5'-R(*UP*UP*UP*U)-3') | Drosophila melanogaster | Crystal structure of DmTailor in complex with U6 RNA | X-ray diffraction | 2 | 2018-12-05 | |||
| 17 | 5ZSA|1|C | RNA (5'-R(P*UP*UP*UP*U)-3') | synthetic construct | Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU | X-ray diffraction | 2.5 | 2019-01-30 | |||
| 18 | 5ZSA|1|D | RNA (5'-R(P*UP*UP*UP*U)-3') | synthetic construct | Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU | X-ray diffraction | 2.5 | 2019-01-30 | |||
| 19 | 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 | ||||
| 20 | 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 | ||||
| 21 | 4Y91|1|O | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | synthetic construct | Crystal Structure of a Thermotoga maritima Hfq homolog | X-ray diffraction | 2.66 | 2016-03-16 | |||
| 22 | 4Y91|1|N | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | synthetic construct | Crystal Structure of a Thermotoga maritima Hfq homolog | X-ray diffraction | 2.66 | 2016-03-16 | |||
| 23 | 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 | ||||
| 24 | 1N34|1|Z | A-SITE MESSENGER RNA FRAGMENT | Thermus thermophilus | 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 | |||
| 25 | 3PF5|1|S | hexaribouracil (rU6) | Crystal structure of Bs-CspB in complex with rU6 | X-ray diffraction | 1.68 | 2011-09-21 | ||||
| 26 | 6PPN|1|A | Mimic of unprocessed U6 snRNA | synthetic construct | Structure of S. pombe Lsm2-8 with unprocessed U6 snRNA | X-ray diffraction | 1.91 | 2020-06-17 | |||
| 27 | 6PPN|1|I | Mimic of unprocessed U6 snRNA | synthetic construct | Structure of S. pombe Lsm2-8 with unprocessed U6 snRNA | X-ray diffraction | 1.91 | 2020-06-17 | |||
| 28 | 7DUH|1|Y | RNA (5'-R(*UP*UP*UP*UP*UP*U)-3') | Thermus thermophilus | Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''AC bound | X-ray diffraction | 3.75 | 2022-01-26 | |||
| 29 | 6M7D|1|B | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | synthetic construct | Structure of ncleoprotein of sendai virus | Electron microscopy | 2.9 | 2021-03-24 | |||
| 30 | 7EWQ|1|B | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | Mumps orthorubulavirus | Structure of Mumps virus nucleocapsid ring | Electron microscopy | 3.5 | 2021-06-23 | |||
| 31 | 7QDZ|1|E | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | Homo sapiens | 80S-bound human SKI complex in the closed state | Electron microscopy | 3.6 | 2022-02-09 | |||
| 32 | 5Z9W|1|R | RNA (6-MER) | synthetic construct | Ebola virus nucleoprotein-RNA complex | Electron microscopy | 3.6 | 2018-10-24 | |||
| 33 | 7NSJ|1|AX | mRNA | Sus scrofa | 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*) | Electron microscopy | 3.9 | 2021-06-02 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_74924.16 | NR_4.0_74924.15 | 3.217 | (32) 2HYI|1|L, 2HYI|1|F, 1N34|1|Z, 7NSJ|1|AX, 7EWQ|1|B, 7DUH|1|Y, 6WRE|1|D, 6PPN|1|I, 6PPN|1|A, 6M7D|1|B, 6I0U|1|B, 6G2K|1|R, 5ZSA|1|D, 5ZSA|1|C, 5Z9W|1|R, 5SZE|1|C, 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 | (1) 7QDZ|1|E | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_4.0_74924.16 | NR_4.0_74924.17 | 3.221 | (33) 3EX7|1|J, 4NL3|1|R, 5Z9W|1|R, 6WRE|1|D, 3EX7|1|F, 4ALP|1|E, 5SZE|1|C, 6PPN|1|I, 2HYI|1|L, 3PF5|1|S, 5ELX|1|B, 6PPN|1|A, 2HYI|1|F, 3PF5|1|R, 5BTE|1|D, 6M7D|1|B, 1N34|1|Z, 3PEY|1|B, 5BTE|1|C, 6I0U|1|B, 7QDZ|1|E, 3PEW|1|B, 4Y91|1|O, 6G2K|1|R, 7NSJ|1|AX, 3O8R|1|C, 4Y91|1|N, 5ZSA|1|D, 7EWQ|1|B, 3O8C|1|C, 4NL3|1|Z, 5ZSA|1|C, 7DUH|1|Y | (0) | (2) 7F1M|1|S, 7F1M|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 |
|---|---|---|---|---|---|
| 1 | 4ALP|1|E | The Lin28b Cold shock domain in complex with hexauridine | X-RAY DIFFRACTION | 1.48 | 6 |
| 2 | 5ZSA|1|C | Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU | X-RAY DIFFRACTION | 2.5 | 4 |
| 3 | 5ZSA|1|D | Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU | X-RAY DIFFRACTION | 2.5 | 4 |
| 4 | 6I0U|1|B | Crystal structure of DmTailor in complex with U6 RNA | X-RAY DIFFRACTION | 2 | 4 |
| 5 | 4NL3|1|R | Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-RAY DIFFRACTION | 3.1 | 6 |
| 6 | 4NL3|1|Z | Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-RAY DIFFRACTION | 3.1 | 6 |
| 7 | 4Y91|1|O | Crystal Structure of a Thermotoga maritima Hfq homolog | X-RAY DIFFRACTION | 2.66 | 6 |
| 8 | 4Y91|1|N | Crystal Structure of a Thermotoga maritima Hfq homolog | X-RAY DIFFRACTION | 2.66 | 6 |
| 9 | 6PPN|1|I | Structure of S. pombe Lsm2-8 with unprocessed U6 snRNA | X-RAY DIFFRACTION | 1.91 | 5 |
| 10 | 6PPN|1|A | Structure of S. pombe Lsm2-8 with unprocessed U6 snRNA | X-RAY DIFFRACTION | 1.91 | 5 |
| 11 | 3PF5|1|R | Crystal structure of Bs-CspB in complex with rU6 | X-RAY DIFFRACTION | 1.68 | 9 |
| 12 | 7NSJ|1|AX | 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*) | ELECTRON MICROSCOPY | 3.9 | 6 |
| 13 | 7EWQ|1|B | Structure of Mumps virus nucleocapsid ring | ELECTRON MICROSCOPY | 3.5 | 6 |
| 14 | 6M7D|1|B | Structure of ncleoprotein of sendai virus | ELECTRON MICROSCOPY | 2.9 | 6 |
| 15 | 3O8R|1|C | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-RAY DIFFRACTION | 2.3 | 5 |
| 16 | 7QDZ|1|E | 80S-bound human SKI complex in the closed state | ELECTRON MICROSCOPY | 3.6 | 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 | 3EX7|1|J | The crystal structure of EJC in its transition state | X-RAY DIFFRACTION | 2.3 | 6 |
| 19 | 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 |
| 20 | 3EX7|1|F | The crystal structure of EJC in its transition state | X-RAY DIFFRACTION | 2.3 | 6 |
| 21 | 3PEY|1|B | S. cerevisiae Dbp5 bound to RNA and ADP BeF3 | X-RAY DIFFRACTION | 1.4 | 6 |
| 22 | 5ELX|1|B | S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3 | X-RAY DIFFRACTION | 1.81 | 6 |
| 23 | 3PEW|1|B | S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3 | X-RAY DIFFRACTION | 1.5 | 6 |
| 24 | 7DUH|1|Y | Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''AC bound | X-RAY DIFFRACTION | 3.75 | 6 |
| 25 | 1N34|1|Z | 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 |
| 26 | 3O8C|1|C | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-RAY DIFFRACTION | 2 | 5 |
| 27 | 3PF5|1|S | Crystal structure of Bs-CspB in complex with rU6 | X-RAY DIFFRACTION | 1.68 | 1 |
| 28 | 5BTE|1|C | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-RAY DIFFRACTION | 2.4 | 4 |
| 29 | 5BTE|1|D | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-RAY DIFFRACTION | 2.4 | 4 |
| 30 | 5Z9W|1|R | Ebola virus nucleoprotein-RNA complex | ELECTRON MICROSCOPY | 3.6 | 6 |
| 31 | 6G2K|1|R | Structure of HuR RRM3 in complex with RNA (UUUUUU) | X-RAY DIFFRACTION | 2.01 | 6 |
| 32 | 6WRE|1|D | Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion | X-RAY DIFFRACTION | 2 | 3 |
| 33 | 5SZE|1|C | Crystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5A | X-RAY DIFFRACTION | 1.5 | 3 |