Equivalence class NR_all_34359.6 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 | 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 | ||||
| 5 | 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 | |||
| 6 | 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 | |||
| 7 | 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 | ||||
| 8 | 7KED|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with unnatural base dTPT3 | X-ray diffraction | 3.6 | 10 | 2021-06-23 | |||
| 9 | 2NVZ|1|R | 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' | synthetic construct | RNA Polymerase II elongation complex with UTP, updated 11/2006 | X-ray diffraction | 4.3 | 10 | 2006-12-19 | |||
| 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 | 1R9S|1|R | RNA strand | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE | X-ray diffraction | 4.25 | 10 | 2004-11-16 | ||||
| 15 | 7OO3|1|P | RNA | Homo sapiens | Pol II-CSB-CSA-DDB1-UVSSA (Structure1) | Electron microscopy | 2.8 | 10 | 2021-10-06 | |||
| 16 | 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 | |||
| 17 | 6H68|1|R | RNA | Saccharomyces cerevisiae | Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) with fully-ordered A49 | Electron microscopy | 4.6 | 10 | 2018-08-29 | |||
| 18 | 5VVR|1|R | RNA | Saccharomyces cerevisiae | Ternary complex of RNA Pol II, transcription scaffold and Rad26 | Electron microscopy | 5.8 | 10 | 2017-11-22 | |||
| 19 | 5VVS|1|R | RNA | Saccharomyces cerevisiae | RNA pol II elongation complex | Electron microscopy | 6.4 | 10 | 2017-11-22 |
Release history
| Release | 3.199 |
|---|---|
| Date | 2021-10-06 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_all_34359.6 | NR_all_34359.5 | 3.199 | (18) 1R9S|1|R, 1R9T|1|R, 1SFO|1|R, 2E2H|1|R, 2E2I|1|R, 2NVQ|1|R, 2NVX|1|R, 2NVZ|1|R, 2YU9|1|R, 5VVR|1|R, 5VVS|1|R, 6H67|1|R, 6H68|1|R, 6UPZ|1|R, 6UQ0|1|R, 7KED|1|R, 7KEE|1|R, 7KEF|1|R | (1) 7OO3|1|P | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_all_34359.6 | NR_all_34359.7 | 3.200 | (19) 1R9S|1|R, 1R9T|1|R, 1SFO|1|R, 2E2H|1|R, 2E2I|1|R, 2NVQ|1|R, 2NVX|1|R, 2NVZ|1|R, 2YU9|1|R, 5VVR|1|R, 5VVS|1|R, 6H67|1|R, 6H68|1|R, 6UPZ|1|R, 6UQ0|1|R, 7KED|1|R, 7KEE|1|R, 7KEF|1|R, 7OO3|1|P | (0) | (1) 7OOB|1|P |
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 | 5VVS|1|R | RNA pol II elongation complex | ELECTRON MICROSCOPY | 6.4 | 10 | |
| 2 | 6H67|1|R | Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) | ELECTRON MICROSCOPY | 3.6 | 9 | |
| 3 | 7KEE|1|R | RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site | X-RAY DIFFRACTION | 3.45 | 10 | |
| 4 | 7KED|1|R | RNA polymerase II elongation complex with unnatural base dTPT3 | X-RAY DIFFRACTION | 3.6 | 10 | |
| 5 | 6UQ0|1|R | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4 | X-RAY DIFFRACTION | 3.56 | 9 | |
| 6 | 2NVZ|1|R | RNA Polymerase II elongation complex with UTP, updated 11/2006 | X-RAY DIFFRACTION | 4.3 | 10 | |
| 7 | 2E2H|1|R | RNA polymerase II elongation complex at 5 mM Mg2+ with GTP | X-RAY DIFFRACTION | 3.95 | 10 | |
| 8 | 7KEF|1|R | RNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state | X-RAY DIFFRACTION | 3.89 | 10 | |
| 9 | 6H68|1|R | Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) with fully-ordered A49 | ELECTRON MICROSCOPY | 4.6 | 10 | |
| 10 | 1R9S|1|R | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE | X-RAY DIFFRACTION | 4.25 | 10 | |
| 11 | 1R9T|1|R | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE | X-RAY DIFFRACTION | 3.5 | 10 | |
| 12 | 1SFO|1|R | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX | X-RAY DIFFRACTION | 3.61 | 10 | |
| 13 | 2NVX|1|R | RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP | X-RAY DIFFRACTION | 3.6 | 10 | |
| 14 | 2E2I|1|R | RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTP | X-RAY DIFFRACTION | 3.41 | 10 | |
| 15 | 2YU9|1|R | RNA polymerase II elongation complex in 150 mm MG+2 with UTP | X-RAY DIFFRACTION | 3.4 | 10 | |
| 16 | 2NVQ|1|R | RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP | X-RAY DIFFRACTION | 2.9 | 10 | |
| 17 | 7OO3|1|P | Pol II-CSB-CSA-DDB1-UVSSA (Structure1) | ELECTRON MICROSCOPY | 2.8 | 10 | |
| 18 | 5VVR|1|R | Ternary complex of RNA Pol II, transcription scaffold and Rad26 | ELECTRON MICROSCOPY | 5.8 | 10 | |
| 19 | 6UPZ|1|R | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3 | X-RAY DIFFRACTION | 3.1 | 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.
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