Equivalence class NR_4.0_34359.12 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2NVQ|1|R (rep) | 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' | synthetic construct | RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP | X-ray diffraction | 2.9 | 10 | 2006-12-12 | |||
| 2 | 6UPZ|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3 | X-ray diffraction | 3.1 | 10 | 2020-06-10 | |||
| 3 | 2NVX|1|R | 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' | RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP | X-ray diffraction | 3.6 | 10 | 2006-12-19 | ||||
| 4 | 8UKT|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with Fapy-dG lesion with AMP added | X-ray diffraction | 3.6 | 10 | 2024-04-24 | |||
| 5 | 2E2I|1|R | 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' | RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTP | X-ray diffraction | 3.41 | 10 | 2006-12-19 | ||||
| 6 | 6UQ0|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4 | X-ray diffraction | 3.56 | 9 | 2020-06-10 | |||
| 7 | 7KEE|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site | X-ray diffraction | 3.45 | 10 | 2021-06-23 | |||
| 8 | 2E2H|1|R | 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' | RNA polymerase II elongation complex at 5 mM Mg2+ with GTP | X-ray diffraction | 3.95 | 10 | 2006-12-12 | ||||
| 9 | 7KED|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with unnatural base dTPT3 | X-ray diffraction | 3.6 | 10 | 2021-06-23 | |||
| 10 | 7KEF|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state | X-ray diffraction | 3.89 | 10 | 2021-06-23 | |||
| 11 | 1SFO|1|R | RNA STRAND | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX | X-ray diffraction | 3.61 | 10 | 2004-03-02 | ||||
| 12 | 1R9T|1|R | RNA strand | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE | X-ray diffraction | 3.5 | 10 | 2004-11-16 | ||||
| 13 | 2YU9|1|R | 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' | synthetic construct | RNA polymerase II elongation complex in 150 mm MG+2 with UTP | X-ray diffraction | 3.4 | 10 | 2007-04-24 | |||
| 14 | 9BVT|1|X | RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3') | synthetic construct | RNA Pol II - High Mn(+2) concentration | X-ray diffraction | 3.4 | 10 | 2024-10-02 | |||
| 15 | 8B3D|1|P | RNA | Homo sapiens | Structure of the Pol II-TCR-ELOF1 complex. | Electron microscopy | 2.6 | 10 | 2023-09-27 | |||
| 16 | 7OOB|1|P | RNA | Homo sapiens | Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2) | Electron microscopy | 2.7 | 10 | 2021-10-13 | |||
| 17 | 7OO3|1|P | RNA | Homo sapiens | Pol II-CSB-CSA-DDB1-UVSSA (Structure1) | Electron microscopy | 2.8 | 10 | 2021-10-06 | |||
| 18 | 8B3F|1|P | RNA | Homo sapiens | Pol II-CSB-CSA-DDB1-ELOF1 | Electron microscopy | 3.1 | 10 | 2023-09-27 | |||
| 19 | 8TVY|1|R | RNA | synthetic construct | Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) | Electron microscopy | 3.1 | 10 | 2024-01-24 | |||
| 20 | 8TUG|1|R | RNA | synthetic construct | Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) | Electron microscopy | 3.5 | 10 | 2024-01-24 | |||
| 21 | 8TVW|1|R | RNA | synthetic construct | Cryo-EM structure of CPD-stalled Pol II (conformation 1) | Electron microscopy | 3.6 | 10 | 2024-01-24 | |||
| 22 | 8TVP|1|R | RNA | synthetic construct | Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) | Electron microscopy | 3.7 | 10 | 2024-01-24 | |||
| 23 | 8TVX|1|R | RNA | synthetic construct | Cryo-EM structure of CPD-stalled Pol II (Conformation 2) | Electron microscopy | 3.7 | 10 | 2024-01-24 | |||
| 24 | 6H67|1|R | RNA | Saccharomyces cerevisiae | Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) | Electron microscopy | 3.6 | 9 | 2018-08-29 | |||
| 25 | 7Z2Z|1|R | RNA | Saccharomyces cerevisiae S288C | Structure of yeast RNA Polymerase III-DNA-Ty1 integrase complex (Pol III-DNA-IN1) at 3.1 A | Electron microscopy | 3.07 | 3 | 2023-04-05 |
Release history
| Release | 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 | 2024-10-02 | 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 | 9BVT|1|X | RNA Pol II - High Mn(+2) concentration | X-RAY DIFFRACTION | 3.4 | 10 | |
| 2 | 7Z2Z|1|R | Structure of yeast RNA Polymerase III-DNA-Ty1 integrase complex (Pol III-DNA-IN1) at 3.1 A | ELECTRON MICROSCOPY | 3.07 | 3 | |
| 3 | 7KED|1|R | RNA polymerase II elongation complex with unnatural base dTPT3 | X-RAY DIFFRACTION | 3.6 | 10 | |
| 4 | 6UQ0|1|R | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4 | X-RAY DIFFRACTION | 3.56 | 9 | |
| 5 | 8TVW|1|R | Cryo-EM structure of CPD-stalled Pol II (conformation 1) | ELECTRON MICROSCOPY | 3.6 | 10 | |
| 6 | 8TVX|1|R | Cryo-EM structure of CPD-stalled Pol II (Conformation 2) | ELECTRON MICROSCOPY | 3.7 | 10 | |
| 7 | 8TUG|1|R | Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state) | ELECTRON MICROSCOPY | 3.5 | 10 | |
| 8 | 8TVY|1|R | Cryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state) | ELECTRON MICROSCOPY | 3.1 | 10 | |
| 9 | 8B3D|1|P | Structure of the Pol II-TCR-ELOF1 complex. | ELECTRON MICROSCOPY | 2.6 | 10 | |
| 10 | 8B3F|1|P | Pol II-CSB-CSA-DDB1-ELOF1 | ELECTRON MICROSCOPY | 3.1 | 10 | |
| 11 | 7OOB|1|P | Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2) | ELECTRON MICROSCOPY | 2.7 | 10 | |
| 12 | 7OO3|1|P | Pol II-CSB-CSA-DDB1-UVSSA (Structure1) | ELECTRON MICROSCOPY | 2.8 | 10 | |
| 13 | 2NVQ|1|R | RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP | X-RAY DIFFRACTION | 2.9 | 10 | |
| 14 | 8TVP|1|R | Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state) | ELECTRON MICROSCOPY | 3.7 | 10 | |
| 15 | 6H67|1|R | Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) | ELECTRON MICROSCOPY | 3.6 | 9 | |
| 16 | 7KEE|1|R | RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site | X-RAY DIFFRACTION | 3.45 | 10 | |
| 17 | 7KEF|1|R | RNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state | X-RAY DIFFRACTION | 3.89 | 10 | |
| 18 | 2E2H|1|R | RNA polymerase II elongation complex at 5 mM Mg2+ with GTP | X-RAY DIFFRACTION | 3.95 | 10 | |
| 19 | 2YU9|1|R | RNA polymerase II elongation complex in 150 mm MG+2 with UTP | X-RAY DIFFRACTION | 3.4 | 10 | |
| 20 | 2E2I|1|R | RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTP | X-RAY DIFFRACTION | 3.41 | 10 | |
| 21 | 2NVX|1|R | RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP | X-RAY DIFFRACTION | 3.6 | 10 | |
| 22 | 1SFO|1|R | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX | X-RAY DIFFRACTION | 3.61 | 10 | |
| 23 | 1R9T|1|R | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE | X-RAY DIFFRACTION | 3.5 | 10 | |
| 24 | 6UPZ|1|R | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3 | X-RAY DIFFRACTION | 3.1 | 10 | |
| 25 | 8UKT|1|R | RNA polymerase II elongation complex with Fapy-dG lesion with AMP added | X-RAY DIFFRACTION | 3.6 | 10 |
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: