Equivalence class NR_all_33912.6 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 7RIQ|1|R (rep) | RNA | synthetic construct | RNA polymerase II elongation complex scaffold 1 without polyamide | X-ray diffraction | 3 | 9 | 2022-01-12 | |||
| 2 | 7RIM|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 | X-ray diffraction | 2.9 | 9 | 2022-01-12 | |||
| 3 | 3S17|1|R | RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*G)-3') | RNA Polymerase II Initiation Complex with a 9-nt RNA | X-ray diffraction | 3.2 | 9 | 2011-08-10 | ||||
| 4 | 6UPY|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 2E | X-ray diffraction | 3.4 | 9 | 2020-06-10 | |||
| 5 | 6UQ2|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with dG in state 1 | X-ray diffraction | 3.2 | 9 | 2020-06-10 | |||
| 6 | 6UPX|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 1 | X-ray diffraction | 3.4 | 9 | 2020-06-10 | |||
| 7 | 8UKS|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with Fapy-dG lesion soaking with CTP before chemistry | X-ray diffraction | 3.4 | 9 | 2024-04-24 | |||
| 8 | 2E2J|1|R | 5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*G)-3' | synthetic construct | RNA polymerase II elongation complex in 5 mM Mg+2 with GMPCPP | X-ray diffraction | 3.5 | 9 | 2006-12-12 | |||
| 9 | 8UKQ|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with Fapy-dG lesion in apo state | X-ray diffraction | 3.5 | 9 | 2024-04-24 | |||
| 10 | 8UKR|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with Fapy-dG lesion soaking with ATP before chemistry | X-ray diffraction | 3.78 | 9 | 2024-04-24 | |||
| 11 | 8SY7|1|R | RNA oligomer | synthetic construct | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-STP base pair in the active site | Electron microscopy | 2.65 | 9 | 2023-12-27 | |||
| 12 | 8SY5|1|R | RNA oligomer | synthetic construct | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dS-BTP base pair in the active site | Electron microscopy | 2.7 | 9 | 2023-12-27 | |||
| 13 | 9JA1|1|R | RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*G)-3') | synthetic construct | The RNA polymerase II elongation complex from Saccharomyces cerevisiae | Electron microscopy | 2.98 | 9 | 2024-09-04 | |||
| 14 | 6O6C|1|K | RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*G)-3') | Saccharomyces cerevisiae | RNA polymerase II elongation complex arrested at a CPD lesion | Electron microscopy | 3.1 | 9 | 2019-06-26 | |||
| 15 | 8TXO|1|R | RNA oligomer | synthetic construct | E. coli DNA-directed RNA polymerase transcription elongation complex bound to the unnatural dZ-PTP base pair in the active site | Electron microscopy | 3.1 | 9 | 2024-01-24 | |||
| 16 | 8SY6|1|R | RNA oligomer | synthetic construct | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site | Electron microscopy | 3.28 | 9 | 2023-12-27 |
Release history
| Release | 3.351 | 3.352 | 3.353 | 3.354 | 3.355 | 3.356 | 3.357 | 3.358 | 3.359 | 3.360 | 3.361 | 3.362 | 3.363 | 3.364 | 3.365 | 3.366 | 3.367 | 3.368 | 3.369 | 3.370 | 3.371 | 3.372 | 3.373 | 3.374 | 3.375 | 3.376 | 3.377 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2024-09-04 | 2024-09-11 | 2024-09-18 | 2024-09-25 | 2024-10-02 | 2024-10-09 | 2024-10-16 | 2024-10-23 | 2024-10-30 | 2024-11-06 | 2024-11-13 | 2024-11-20 | 2024-11-27 | 2024-12-04 | 2024-12-11 | 2024-12-18 | 2024-12-25 | 2025-01-01 | 2025-01-08 | 2025-01-15 | 2025-01-22 | 2025-01-29 | 2025-02-05 | 2025-02-12 | 2025-02-19 | 2025-02-26 | 2025-03-05 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
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 | 2E2J|1|R | RNA polymerase II elongation complex in 5 mM Mg+2 with GMPCPP | X-RAY DIFFRACTION | 3.5 | 9 | |
| 2 | 6UPY|1|R | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 2E | X-RAY DIFFRACTION | 3.4 | 9 | |
| 3 | 6UPX|1|R | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 1 | X-RAY DIFFRACTION | 3.4 | 9 | |
| 4 | 3S17|1|R | RNA Polymerase II Initiation Complex with a 9-nt RNA | X-RAY DIFFRACTION | 3.2 | 9 | |
| 5 | 7RIQ|1|R | RNA polymerase II elongation complex scaffold 1 without polyamide | X-RAY DIFFRACTION | 3 | 9 | |
| 6 | 6UQ2|1|R | RNA polymerase II elongation complex with dG in state 1 | X-RAY DIFFRACTION | 3.2 | 9 | |
| 7 | 9JA1|1|R | The RNA polymerase II elongation complex from Saccharomyces cerevisiae | ELECTRON MICROSCOPY | 2.98 | 9 | |
| 8 | 7RIM|1|R | RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 | X-RAY DIFFRACTION | 2.9 | 9 | |
| 9 | 8UKS|1|R | RNA polymerase II elongation complex with Fapy-dG lesion soaking with CTP before chemistry | X-RAY DIFFRACTION | 3.4 | 9 | |
| 10 | 8UKR|1|R | RNA polymerase II elongation complex with Fapy-dG lesion soaking with ATP before chemistry | X-RAY DIFFRACTION | 3.78 | 9 | |
| 11 | 8UKQ|1|R | RNA polymerase II elongation complex with Fapy-dG lesion in apo state | X-RAY DIFFRACTION | 3.5 | 9 | |
| 12 | 6O6C|1|K | RNA polymerase II elongation complex arrested at a CPD lesion | ELECTRON MICROSCOPY | 3.1 | 9 | |
| 13 | 8SY5|1|R | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dS-BTP base pair in the active site | ELECTRON MICROSCOPY | 2.7 | 9 | |
| 14 | 8SY7|1|R | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-STP base pair in the active site | ELECTRON MICROSCOPY | 2.65 | 9 | |
| 15 | 8TXO|1|R | E. coli DNA-directed RNA polymerase transcription elongation complex bound to the unnatural dZ-PTP base pair in the active site | ELECTRON MICROSCOPY | 3.1 | 9 | |
| 16 | 8SY6|1|R | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site | ELECTRON MICROSCOPY | 3.28 | 9 |
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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