Equivalence class NR_4.0_74924.13 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 3 | 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 | 6 | 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 | 6 | 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 | 6 | 2015-07-22 | |||
| 13 | 3PF5|1|R | hexaribouracil (rU6) | Crystal structure of Bs-CspB in complex with rU6 | X-ray diffraction | 1.68 | 5 | 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 | 6 | 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 | 5 | 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 | 4 | 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 | 4 | 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 | 4 | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 6 | 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 | 4 | 2002-11-29 | |||
| 25 | 3PF5|1|S | hexaribouracil (rU6) | Crystal structure of Bs-CspB in complex with rU6 | X-ray diffraction | 1.68 | 1 | 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 | 5 | 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 | 5 | 2020-06-17 | |||
| 28 | 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 | 6 | 2021-03-24 | |||
| 29 | 5Z9W|1|R | RNA (6-MER) | synthetic construct | Ebola virus nucleoprotein-RNA complex | Electron microscopy | 3.6 | 6 | 2018-10-24 | |||
| 30 | 7NSJ|1|AX | mRNA | Sus scrofa | 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*) | Electron microscopy | 3.9 | 6 | 2021-06-02 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_74924.13 | NR_4.0_74924.12 | 3.181 | (29) 1N34|1|Z, 2HYI|1|F, 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, 4ALP|1|E, 4NL3|1|R, 4NL3|1|Z, 4Y91|1|N, 4Y91|1|O, 5BTE|1|C, 5BTE|1|D, 5ELX|1|B, 5SZE|1|C, 5Z9W|1|R, 5ZSA|1|C, 5ZSA|1|D, 6G2K|1|R, 6I0U|1|B, 6M7D|1|B, 6PPN|1|A, 6PPN|1|I, 6WRE|1|D | (1) 7NSJ|1|AX | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_4.0_74924.13 | NR_4.0_74924.14 | 3.184 | (30) 1N34|1|Z, 2HYI|1|F, 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, 4ALP|1|E, 4NL3|1|R, 4NL3|1|Z, 4Y91|1|N, 4Y91|1|O, 5BTE|1|C, 5BTE|1|D, 5ELX|1|B, 5SZE|1|C, 5Z9W|1|R, 5ZSA|1|C, 5ZSA|1|D, 6G2K|1|R, 6I0U|1|B, 6M7D|1|B, 6PPN|1|A, 6PPN|1|I, 6WRE|1|D, 7NSJ|1|AX | (0) | (1) 7EWQ|1|B |
Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.
| #S | View | PDB | Title | Method | Resolution | #NTs |
|---|---|---|---|---|---|---|
| 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 | 4NL3|1|Z | Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA | X-RAY DIFFRACTION | 3.1 | 6 | |
| 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 | 6PPN|1|I | Structure of S. pombe Lsm2-8 with unprocessed U6 snRNA | X-RAY DIFFRACTION | 1.91 | 5 | |
| 9 | 6PPN|1|A | Structure of S. pombe Lsm2-8 with unprocessed U6 snRNA | X-RAY DIFFRACTION | 1.91 | 5 | |
| 10 | 6G2K|1|R | Structure of HuR RRM3 in complex with RNA (UUUUUU) | X-RAY DIFFRACTION | 2.01 | 6 | |
| 11 | 7NSJ|1|AX | 55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*) | ELECTRON MICROSCOPY | 3.9 | 6 | |
| 12 | 3PF5|1|R | Crystal structure of Bs-CspB in complex with rU6 | X-RAY DIFFRACTION | 1.68 | 5 | |
| 13 | 6I0U|1|B | Crystal structure of DmTailor in complex with U6 RNA | X-RAY DIFFRACTION | 2 | 4 | |
| 14 | 3O8R|1|C | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-RAY DIFFRACTION | 2.3 | 6 | |
| 15 | 3PF5|1|S | Crystal structure of Bs-CspB in complex with rU6 | X-RAY DIFFRACTION | 1.68 | 1 | |
| 16 | 3O8C|1|C | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | X-RAY DIFFRACTION | 2 | 6 | |
| 17 | 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 | |
| 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 | 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 | |
| 21 | 3EX7|1|F | The crystal structure of EJC in its transition state | X-RAY DIFFRACTION | 2.3 | 6 | |
| 22 | 3PEY|1|B | S. cerevisiae Dbp5 bound to RNA and ADP BeF3 | X-RAY DIFFRACTION | 1.4 | 6 | |
| 23 | 5ELX|1|B | S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3 | X-RAY DIFFRACTION | 1.81 | 6 | |
| 24 | 3PEW|1|B | S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3 | X-RAY DIFFRACTION | 1.5 | 6 | |
| 25 | 6M7D|1|B | Structure of ncleoprotein of sendai virus | ELECTRON MICROSCOPY | 2.9 | 6 | |
| 26 | 5BTE|1|C | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-RAY DIFFRACTION | 2.4 | 6 | |
| 27 | 5BTE|1|D | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | X-RAY DIFFRACTION | 2.4 | 6 | |
| 28 | 5Z9W|1|R | Ebola virus nucleoprotein-RNA complex | ELECTRON MICROSCOPY | 3.6 | 6 | |
| 29 | 5SZE|1|C | Crystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5A | X-RAY DIFFRACTION | 1.5 | 3 | |
| 30 | 6WRE|1|D | Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion | X-RAY DIFFRACTION | 2 | 5 |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.
Coloring options: