Equivalence class NR_all_26629.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3HK2|1|F (rep) | 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' | Crystal structure of T. thermophilus Argonaute N478 mutant protein complexed with DNA guide strand and 19-nt RNA target strand | X-ray diffraction | 2.8 | 2009-10-06 | ||||
| 2 | 3HK2|1|D | 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' | Crystal structure of T. thermophilus Argonaute N478 mutant protein complexed with DNA guide strand and 19-nt RNA target strand | X-ray diffraction | 2.8 | 2009-10-06 | ||||
| 3 | 5UX0|1|B | RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3') | synthetic construct | Synthetic | X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA | X-ray diffraction | 3.2 | 2017-05-03 | ||
| 4 | 5UX0|1|E | RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3') | synthetic construct | Synthetic | X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA | X-ray diffraction | 3.2 | 2017-05-03 | ||
| 5 | 3HVR|1|D | 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' | Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site | X-ray diffraction | 3.21 | 2009-10-06 | ||||
| 6 | 3HM9|1|Y | 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' | Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand | X-ray diffraction | 3.3 | 2009-10-06 | ||||
| 7 | 3HVR|1|N | 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' | Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site | X-ray diffraction | 3.21 | 2009-10-06 | ||||
| 8 | 3F73|1|Y | RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3') | Alignment of guide-target seed duplex within an argonaute silencing complex | X-ray diffraction | 3 | 2008-12-16 | ||||
| 9 | 3HXM|1|Y | RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3') | Structure of an argonaute complexed with guide DNA and target RNA duplex containing two mismatches. | X-ray diffraction | 3.1 | 2009-10-06 | ||||
| 10 | 3F73|1|H | RNA (5'-R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3') | Alignment of guide-target seed duplex within an argonaute silencing complex | X-ray diffraction | 3 | 2008-12-16 | ||||
| 11 | 7V6C|1|F+ 7V6C|1|E | RNA (5'-R(P*CP*CP*UP*CP*UP*CP*U)-3'), RNA (5'-R(P*UP*GP*AP*GP*G)-3') | Drosophila melanogaster | Eukarya | Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex | Electron microscopy | 3.3 | 2022-03-23 |
Release history
| Release | 3.223 | 3.224 | 3.225 | 3.226 | 3.227 | 3.228 | 3.229 | 3.230 | 3.231 | 3.232 | 3.233 | 3.234 | 3.235 | 3.236 | 3.237 | 3.238 | 3.239 | 3.240 | 3.241 | 3.242 | 3.243 | 3.244 | 3.245 | 3.246 | 3.247 | 3.248 | 3.249 | 3.250 | 3.251 | 3.252 | 3.253 | 3.254 | 3.255 | 3.256 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2022-03-23 | 2022-03-30 | 2022-04-06 | 2022-04-13 | 2022-04-20 | 2022-04-27 | 2022-05-04 | 2022-05-11 | 2022-05-18 | 2022-05-25 | 2022-06-01 | 2022-06-08 | 2022-06-15 | 2022-06-22 | 2022-06-29 | 2022-07-06 | 2022-07-13 | 2022-07-20 | 2022-07-27 | 2022-08-03 | 2022-08-10 | 2022-08-17 | 2022-08-24 | 2022-08-31 | 2022-09-07 | 2022-09-14 | 2022-09-21 | 2022-09-28 | 2022-10-05 | 2022-10-12 | 2022-10-19 | 2022-10-26 | 2022-11-02 | 2022-11-09 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_all_26629.2 | NR_all_14902.1 | 3.223 | (2) 5UX0|1|B, 5UX0|1|E | (9) 3HVR|1|N, 3HVR|1|D, 3HM9|1|Y, 3HK2|1|F, 3HK2|1|D, 3F73|1|Y, 3F73|1|H, 7V6C|1|F+7V6C|1|E, 3HXM|1|Y | (0) |
| NR_all_26629.2 | NR_all_26629.1 | 3.223 | (8) 3HVR|1|N, 3HVR|1|D, 3HM9|1|Y, 3HK2|1|F, 3HK2|1|D, 3F73|1|Y, 3F73|1|H, 3HXM|1|Y | (3) 7V6C|1|F+7V6C|1|E, 5UX0|1|E, 5UX0|1|B | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_all_26629.2 | NR_all_26629.3 | 3.257 | (11) 3HM9|1|Y, 3HK2|1|F, 3HK2|1|D, 3F73|1|Y, 3F73|1|H, 7V6C|1|F+7V6C|1|E, 5UX0|1|E, 5UX0|1|B, 3HXM|1|Y, 3HVR|1|N, 3HVR|1|D | (0) | (1) 8DGA|1|F+8DGA|1|E |
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 | 3F73|1|H | Alignment of guide-target seed duplex within an argonaute silencing complex | X-RAY DIFFRACTION | 3 | 12 |
| 2 | 3F73|1|Y | Alignment of guide-target seed duplex within an argonaute silencing complex | X-RAY DIFFRACTION | 3 | 11 |
| 3 | 3HXM|1|Y | Structure of an argonaute complexed with guide DNA and target RNA duplex containing two mismatches. | X-RAY DIFFRACTION | 3.1 | 9 |
| 4 | 3HVR|1|D | Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site | X-RAY DIFFRACTION | 3.21 | 12 |
| 5 | 3HVR|1|N | Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site | X-RAY DIFFRACTION | 3.21 | 10 |
| 6 | 3HK2|1|D | Crystal structure of T. thermophilus Argonaute N478 mutant protein complexed with DNA guide strand and 19-nt RNA target strand | X-RAY DIFFRACTION | 2.8 | 15 |
| 7 | 3HK2|1|F | Crystal structure of T. thermophilus Argonaute N478 mutant protein complexed with DNA guide strand and 19-nt RNA target strand | X-RAY DIFFRACTION | 2.8 | 15 |
| 8 | 3HM9|1|Y | Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand | X-RAY DIFFRACTION | 3.3 | 13 |
| 9 | 7V6C|1|F+7V6C|1|E | Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex | ELECTRON MICROSCOPY | 3.3 | 7 |
| 10 | 5UX0|1|E | X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA | X-RAY DIFFRACTION | 3.2 | 18 |
| 11 | 5UX0|1|B | X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA | X-RAY DIFFRACTION | 3.2 | 20 |