Equivalence class NR_4.0_26629.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | 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 | 15 | 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 | 15 | 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 | X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA | X-ray diffraction | 3.2 | 20 | 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 | X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA | X-ray diffraction | 3.2 | 18 | 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 | 12 | 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 | 13 | 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 | 10 | 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 | 11 | 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 | 9 | 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 | 12 | 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 | Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex | Electron microscopy | 3.3 | 12 | 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_4.0_26629.2 | NR_4.0_14902.1 | 3.223 | (2) 5UX0|1|B, 5UX0|1|E | (9) 3F73|1|H, 3F73|1|Y, 3HK2|1|D, 3HK2|1|F, 3HM9|1|Y, 3HVR|1|D, 3HVR|1|N, 3HXM|1|Y, 7V6C|1|F+7V6C|1|E | (0) |
| NR_4.0_26629.2 | NR_4.0_26629.1 | 3.223 | (8) 3F73|1|H, 3F73|1|Y, 3HK2|1|D, 3HK2|1|F, 3HM9|1|Y, 3HVR|1|D, 3HVR|1|N, 3HXM|1|Y | (3) 5UX0|1|B, 5UX0|1|E, 7V6C|1|F+7V6C|1|E | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_4.0_26629.2 | NR_4.0_26629.3 | 3.257 | (11) 3F73|1|H, 3F73|1|Y, 3HK2|1|D, 3HK2|1|F, 3HM9|1|Y, 3HVR|1|D, 3HVR|1|N, 3HXM|1|Y, 5UX0|1|B, 5UX0|1|E, 7V6C|1|F+7V6C|1|E | (0) | (1) 8DGA|1|F+8DGA|1|E |
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 | 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 | 12 | |
| 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 |
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.
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