Equivalence class NR_3.5_64918.15 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 7SOS|1|B (rep) | RNA (5'-R(*AP*AP*AP*A)-3') | synthetic construct | LaM domain of human LARP1 in complex with AAAA RNA | X-ray diffraction | 1.25 | 4 | 2022-08-03 | |||
| 2 | 6SCE|1|B | cyclic oligoadenylate | synthetic construct | Structure of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate | X-ray diffraction | 1.83 | 4 | 2020-02-19 | |||
| 3 | 6XL1|1|C | cA4 | synthetic construct | crystal structure of cA4-activated Cad1(D294N) | X-ray diffraction | 1.95 | 4 | 2020-12-30 | |||
| 4 | 6SCF|1|I | cyclic oligoadenylate | synthetic construct | A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate | X-ray diffraction | 1.55 | 4 | 2019-10-30 | |||
| 5 | 6SCF|1|K | cyclic oligoadenylate | synthetic construct | A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate | X-ray diffraction | 1.55 | 4 | 2019-10-30 | |||
| 6 | 6YUD|1|K | cyclic tetra-adenylate (cA4) | synthetic construct | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-ray diffraction | 1.84 | 4 | 2020-08-19 | |||
| 7 | 6YUD|1|O | cyclic tetra-adenylate (cA4) | synthetic construct | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-ray diffraction | 1.84 | 4 | 2020-08-19 | |||
| 8 | 6SCF|1|M | cyclic oligoadenylate | synthetic construct | A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate | X-ray diffraction | 1.55 | 4 | 2019-10-30 | |||
| 9 | 6YUD|1|P | cyclic tetra-adenylate (cA4) | synthetic construct | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-ray diffraction | 1.84 | 4 | 2020-08-19 | |||
| 10 | 6SCF|1|L | cyclic oligoadenylate | synthetic construct | A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate | X-ray diffraction | 1.55 | 4 | 2019-10-30 | |||
| 11 | 6YUD|1|M | cyclic tetra-adenylate (cA4) | synthetic construct | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-ray diffraction | 1.84 | 4 | 2020-08-19 | |||
| 12 | 6YUD|1|Q | cyclic tetra-adenylate (cA4) | synthetic construct | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-ray diffraction | 1.84 | 4 | 2020-08-19 | |||
| 13 | 6WXQ|1|E | cyclic tetraadenylate | synthetic construct | Crystal structure of CRISPR-associated transcription factor Csa3 complexed with cA4 | X-ray diffraction | 2.05 | 4 | 2021-11-17 | |||
| 14 | 8BAO|1|C | Cyclic tetra-adenylate (cA4) | synthetic construct | Dysgonamonadaceae bacterium CRISPR ancillary nuclease 2 | X-ray diffraction | 2.06 | 4 | 2022-11-30 | |||
| 15 | 6W11|1|C | cA4 | Saccharolobus solfataricus | The structure of Sulfolobus solfataricus Csa3 in complex with cyclic tetraadenylate (cA4) | X-ray diffraction | 2.46 | 4 | 2021-03-10 | |||
| 16 | 6O6X|1|D | Cyclic RNA cA4 | synthetic construct | Crystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallization | X-ray diffraction | 2.11 | 4 | 2019-07-31 | |||
| 17 | 4BA2|1|R | 5'-R(*AP*AP*AP*AP)-3' | Saccharolobus solfataricus | Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate | X-ray diffraction | 2.5 | 4 | 2012-10-03 | |||
| 18 | 7BDV|1|F | cyclic tetra-adenylate | synthetic construct | Structure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4) | X-ray diffraction | 2.02 | 4 | 2021-03-03 | |||
| 19 | 8B0R|1|D | RNA (5'-R(P*AP*AP*AP*A)-3') | Sulfurihydrogenibium | Structure of the CalpL/cA4 complex | X-ray diffraction | 2.2 | 4 | 2022-11-16 | |||
| 20 | 7BDV|1|H | cyclic tetra-adenylate | synthetic construct | Structure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4) | X-ray diffraction | 2.02 | 4 | 2021-03-03 | |||
| 21 | 6O6X|1|C | Cyclic RNA cA4 | synthetic construct | Crystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallization | X-ray diffraction | 2.11 | 4 | 2019-07-31 | |||
| 22 | 7DID|1|C | RNA (5'-R(*AP*AP*AP*A)-3') | Mycoplasma genitalium G37 | Mycoplasma genitalium RNase R in complex with ribose methylated single-stranded RNA | X-ray diffraction | 1.9 | 4 | 2021-03-17 | |||
| 23 | 6O7B|1|C | Cyclic RNA cA4 | synthetic construct | Crystal structure of Csm1-Csm4 cassette in complex with cA4 | X-ray diffraction | 2.4 | 4 | 2019-07-31 | |||
| 24 | 6O6V|1|C | Cyclic RNA cA4 | synthetic construct | Crystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6 | X-ray diffraction | 2.35 | 4 | 2019-07-31 | |||
| 25 | 6WXX|1|Y | cA4 | synthetic construct | crystal structure of cA4-activated Cad1 | X-ray diffraction | 3 | 4 | 2020-12-30 | |||
| 26 | 6WXX|1|X | cA4 | synthetic construct | crystal structure of cA4-activated Cad1 | X-ray diffraction | 3 | 4 | 2020-12-30 | |||
| 27 | 6R7B|1|D | RNA (5'-R(P*AP*AP*AP*A)-3') | synthetic construct | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 1 | X-ray diffraction | 3.12 | 4 | 2019-10-02 | |||
| 28 | 6R9R|1|D | DNA (5'-R(P*AP*AP*AP*A)-3') | synthetic construct | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2 | X-ray diffraction | 2.7 | 4 | 2019-10-02 | |||
| 29 | 6OV0|1|E | RNA (5'-R(*AP*AP*AP*(A23))-3') | synthetic construct | Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 | X-ray diffraction | 2.8 | 4 | 2019-07-31 | |||
| 30 | 7YGH|1|C | RNA (5'-R(P*AP*AP*AP*A)-3') | synthetic construct | Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with cyclic-tetraadenylate (cA4) | X-ray diffraction | 3.11 | 4 | 2023-02-15 | |||
| 31 | 7YGL|1|C | RNA (5'-R(*AP*AP*AP*(A23))-3') | synthetic construct | Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with A4>p cleavage intermediate | X-ray diffraction | 2.5 | 4 | 2023-02-15 | |||
| 32 | 6OV0|1|H | RNA (5'-R(*AP*AP*AP*(A23))-3') | synthetic construct | Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 | X-ray diffraction | 2.8 | 4 | 2019-07-31 | |||
| 33 | 6OV0|1|G | RNA (5'-R(*AP*AP*AP*(A23))-3') | synthetic construct | Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 | X-ray diffraction | 2.8 | 3 | 2019-07-31 | |||
| 34 | 6O6V|1|D | Cyclic RNA cA4 | synthetic construct | Crystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6 | X-ray diffraction | 2.35 | 4 | 2019-07-31 | |||
| 35 | 6OV0|1|F | RNA (5'-R(*AP*AP*AP*(A23))-3') | synthetic construct | Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 | X-ray diffraction | 2.8 | 3 | 2019-07-31 | |||
| 36 | 6O7B|1|D | Cyclic RNA cA4 | synthetic construct | Crystal structure of Csm1-Csm4 cassette in complex with cA4 | X-ray diffraction | 2.4 | 4 | 2019-07-31 | |||
| 37 | 6R9R|1|E | DNA (5'-R(P*AP*AP*AP*A)-3') | synthetic construct | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2 | X-ray diffraction | 2.7 | 2 | 2019-10-02 | |||
| 38 | 6R7B|1|E | RNA (5'-R(P*AP*AP*AP*A)-3') | synthetic construct | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 1 | X-ray diffraction | 3.12 | 2 | 2019-10-02 | |||
| 39 | 7Z55|1|CCC | Cyclic RNA cA4 | synthetic construct | Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in complex with its substrate | X-ray diffraction | 1.664 | 4 | 2022-11-23 | |||
| 40 | 6O7I|1|I | RNA (5'-R(P*AP*AP*AP*A)-3') | synthetic construct | Cryo-EM structure of Csm-crRNA-target RNA ternary bigger complex in complex with cA4 in type III-A CRISPR-Cas system | Electron microscopy | 3.2 | 4 | 2019-07-31 | |||
| 41 | 6O7H|1|K | Cyclic DNA cA4 | synthetic construct | Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas system | Electron microscopy | 2.9 | 4 | 2019-07-31 |
Release history
| Release | 3.270 | 3.271 | 3.272 | 3.273 | 3.274 | 3.275 | 3.276 | 3.277 | 3.278 | 3.279 | 3.280 | 3.281 | 3.282 | 3.283 | 3.284 | 3.285 | 3.286 | 3.287 | 3.288 | 3.289 | 3.290 | 3.291 | 3.292 | 3.293 | 3.294 | 3.295 | 3.296 | 3.297 | 3.298 | 3.299 | 3.300 | 3.301 | 3.302 | 3.303 | 3.304 | 3.305 | 3.306 | 3.307 | 3.308 | 3.309 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2023-02-15 | 2023-02-22 | 2023-03-01 | 2023-03-08 | 2023-03-15 | 2023-03-22 | 2023-03-29 | 2023-04-05 | 2023-04-12 | 2023-04-19 | 2023-04-26 | 2023-05-03 | 2023-05-10 | 2023-05-17 | 2023-05-24 | 2023-05-31 | 2023-06-07 | 2023-06-14 | 2023-06-21 | 2023-06-28 | 2023-07-05 | 2023-07-12 | 2023-07-19 | 2023-07-26 | 2023-08-02 | 2023-08-09 | 2023-08-16 | 2023-08-23 | 2023-08-30 | 2023-09-06 | 2023-09-13 | 2023-09-20 | 2023-09-27 | 2023-10-04 | 2023-10-11 | 2023-10-18 | 2023-10-25 | 2023-11-01 | 2023-11-08 | 2023-11-15 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_64918.15 | NR_3.5_64918.14 | 3.270 | (39) 4BA2|1|R, 6O6V|1|C, 6O6V|1|D, 6O6X|1|C, 6O6X|1|D, 6O7B|1|C, 6O7B|1|D, 6O7H|1|K, 6O7I|1|I, 6OV0|1|E, 6OV0|1|F, 6OV0|1|G, 6OV0|1|H, 6R7B|1|D, 6R7B|1|E, 6R9R|1|D, 6R9R|1|E, 6SCE|1|B, 6SCF|1|I, 6SCF|1|K, 6SCF|1|L, 6SCF|1|M, 6W11|1|C, 6WXQ|1|E, 6WXX|1|X, 6WXX|1|Y, 6XL1|1|C, 6YUD|1|K, 6YUD|1|M, 6YUD|1|O, 6YUD|1|P, 6YUD|1|Q, 7BDV|1|F, 7BDV|1|H, 7DID|1|C, 7SOS|1|B, 7Z55|1|CCC, 8B0R|1|D, 8BAO|1|C | (2) 7YGH|1|C, 7YGL|1|C | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_64918.15 | NR_3.5_64918.16 | 3.310 | (41) 4BA2|1|R, 6O6V|1|C, 6O6V|1|D, 6O6X|1|C, 6O6X|1|D, 6O7B|1|C, 6O7B|1|D, 6O7H|1|K, 6O7I|1|I, 6OV0|1|E, 6OV0|1|F, 6OV0|1|G, 6OV0|1|H, 6R7B|1|D, 6R7B|1|E, 6R9R|1|D, 6R9R|1|E, 6SCE|1|B, 6SCF|1|I, 6SCF|1|K, 6SCF|1|L, 6SCF|1|M, 6W11|1|C, 6WXQ|1|E, 6WXX|1|X, 6WXX|1|Y, 6XL1|1|C, 6YUD|1|K, 6YUD|1|M, 6YUD|1|O, 6YUD|1|P, 6YUD|1|Q, 7BDV|1|F, 7BDV|1|H, 7DID|1|C, 7SOS|1|B, 7YGH|1|C, 7YGL|1|C, 7Z55|1|CCC, 8B0R|1|D, 8BAO|1|C | (0) | (6) 8Q3Z|1|X, 8Q40|1|X, 8Q41|1|X, 8Q42|1|X, 8Q43|1|X, 8Q44|1|X |
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 | 4BA2|1|R | Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate | X-RAY DIFFRACTION | 2.5 | 4 | |
| 2 | 7SOS|1|B | LaM domain of human LARP1 in complex with AAAA RNA | X-RAY DIFFRACTION | 1.25 | 4 | |
| 3 | 6O6V|1|D | Crystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6 | X-RAY DIFFRACTION | 2.35 | 4 | |
| 4 | 6O6X|1|C | Crystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallization | X-RAY DIFFRACTION | 2.11 | 4 | |
| 5 | 7BDV|1|H | Structure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4) | X-RAY DIFFRACTION | 2.02 | 4 | |
| 6 | 6WXX|1|X | crystal structure of cA4-activated Cad1 | X-RAY DIFFRACTION | 3 | 4 | |
| 7 | 6WXX|1|Y | crystal structure of cA4-activated Cad1 | X-RAY DIFFRACTION | 3 | 4 | |
| 8 | 6XL1|1|C | crystal structure of cA4-activated Cad1(D294N) | X-RAY DIFFRACTION | 1.95 | 4 | |
| 9 | 7Z55|1|CCC | Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in complex with its substrate | X-RAY DIFFRACTION | 1.664 | 4 | |
| 10 | 6W11|1|C | The structure of Sulfolobus solfataricus Csa3 in complex with cyclic tetraadenylate (cA4) | X-RAY DIFFRACTION | 2.46 | 4 | |
| 11 | 6SCF|1|M | A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate | X-RAY DIFFRACTION | 1.55 | 4 | |
| 12 | 6SCF|1|K | A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate | X-RAY DIFFRACTION | 1.55 | 4 | |
| 13 | 6SCF|1|L | A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate | X-RAY DIFFRACTION | 1.55 | 4 | |
| 14 | 6O7I|1|I | Cryo-EM structure of Csm-crRNA-target RNA ternary bigger complex in complex with cA4 in type III-A CRISPR-Cas system | ELECTRON MICROSCOPY | 3.2 | 4 | |
| 15 | 6O7H|1|K | Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas system | ELECTRON MICROSCOPY | 2.9 | 4 | |
| 16 | 6O7B|1|D | Crystal structure of Csm1-Csm4 cassette in complex with cA4 | X-RAY DIFFRACTION | 2.4 | 4 | |
| 17 | 6R7B|1|D | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 1 | X-RAY DIFFRACTION | 3.12 | 4 | |
| 18 | 6R9R|1|D | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2 | X-RAY DIFFRACTION | 2.7 | 4 | |
| 19 | 6O6X|1|D | Crystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallization | X-RAY DIFFRACTION | 2.11 | 4 | |
| 20 | 6O6V|1|C | Crystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6 | X-RAY DIFFRACTION | 2.35 | 4 | |
| 21 | 6YUD|1|M | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-RAY DIFFRACTION | 1.84 | 4 | |
| 22 | 6YUD|1|Q | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-RAY DIFFRACTION | 1.84 | 4 | |
| 23 | 6YUD|1|K | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-RAY DIFFRACTION | 1.84 | 4 | |
| 24 | 6YUD|1|P | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-RAY DIFFRACTION | 1.84 | 4 | |
| 25 | 6YUD|1|O | Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4) | X-RAY DIFFRACTION | 1.84 | 4 | |
| 26 | 6SCE|1|B | Structure of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate | X-RAY DIFFRACTION | 1.83 | 4 | |
| 27 | 6SCF|1|I | A viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate | X-RAY DIFFRACTION | 1.55 | 4 | |
| 28 | 6WXQ|1|E | Crystal structure of CRISPR-associated transcription factor Csa3 complexed with cA4 | X-RAY DIFFRACTION | 2.05 | 4 | |
| 29 | 7BDV|1|F | Structure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4) | X-RAY DIFFRACTION | 2.02 | 4 | |
| 30 | 8BAO|1|C | Dysgonamonadaceae bacterium CRISPR ancillary nuclease 2 | X-RAY DIFFRACTION | 2.06 | 4 | |
| 31 | 8B0R|1|D | Structure of the CalpL/cA4 complex | X-RAY DIFFRACTION | 2.2 | 4 | |
| 32 | 6OV0|1|H | Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 | X-RAY DIFFRACTION | 2.8 | 4 | |
| 33 | 6OV0|1|E | Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 | X-RAY DIFFRACTION | 2.8 | 4 | |
| 34 | 6O7B|1|C | Crystal structure of Csm1-Csm4 cassette in complex with cA4 | X-RAY DIFFRACTION | 2.4 | 4 | |
| 35 | 7DID|1|C | Mycoplasma genitalium RNase R in complex with ribose methylated single-stranded RNA | X-RAY DIFFRACTION | 1.9 | 4 | |
| 36 | 7YGL|1|C | Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with A4>p cleavage intermediate | X-RAY DIFFRACTION | 2.5 | 4 | |
| 37 | 6R9R|1|E | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2 | X-RAY DIFFRACTION | 2.7 | 2 | |
| 38 | 6OV0|1|F | Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 | X-RAY DIFFRACTION | 2.8 | 3 | |
| 39 | 6R7B|1|E | Crystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 1 | X-RAY DIFFRACTION | 3.12 | 2 | |
| 40 | 7YGH|1|C | Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with cyclic-tetraadenylate (cA4) | X-RAY DIFFRACTION | 3.11 | 4 | |
| 41 | 6OV0|1|G | Crystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6 | X-RAY DIFFRACTION | 2.8 | 3 |
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: