Equivalence class NR_20.0_34359.5 Obsolete
# | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 2006-12-12 | ||||
8 | 7KED|1|R | RNA | synthetic construct | RNA polymerase II elongation complex with unnatural base dTPT3 | X-ray diffraction | 3.6 | 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 | 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 | 2021-06-23 | |||
11 | 1SFO|1|R | RNA STRAND | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX | X-ray diffraction | 3.61 | 2004-03-02 | ||||
12 | 1R9T|1|R | RNA strand | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE | X-ray diffraction | 3.5 | 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 | 2007-04-24 | |||
14 | 1R9S|1|R | RNA strand | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE | X-ray diffraction | 4.25 | 2004-11-16 | ||||
15 | 6H67|1|R | RNA | Saccharomyces cerevisiae | Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) | Electron microscopy | 3.6 | 2018-08-29 | |||
16 | 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 | 2018-08-29 | |||
17 | 5VVR|1|R | RNA | Saccharomyces cerevisiae | Ternary complex of RNA Pol II, transcription scaffold and Rad26 | Electron microscopy | 5.8 | 2017-11-22 | |||
18 | 5VVS|1|R | RNA | Saccharomyces cerevisiae | RNA pol II elongation complex | Electron microscopy | 6.4 | 2017-11-22 |
Release history
Parents
This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
---|---|---|---|---|---|
NR_20.0_34359.5 | NR_20.0_34359.4 | 3.184 | (15) 2NVX|1|R, 2NVQ|1|R, 2E2I|1|R, 6UQ0|1|R, 2E2H|1|R, 6UPZ|1|R, 1SFO|1|R, 6H68|1|R, 1R9T|1|R, 6H67|1|R, 1R9S|1|R, 5VVS|1|R, 5VVR|1|R, 2YU9|1|R, 2NVZ|1|R | (3) 7KED|1|R, 7KEF|1|R, 7KEE|1|R | (0) |
Children
This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
---|---|---|---|---|---|
NR_20.0_34359.5 | NR_20.0_34359.6 | 3.199 | (18) 1R9T|1|R, 7KEF|1|R, 1R9S|1|R, 7KEE|1|R, 7KED|1|R, 6UQ0|1|R, 6UPZ|1|R, 6H68|1|R, 6H67|1|R, 5VVS|1|R, 5VVR|1|R, 2YU9|1|R, 2NVZ|1|R, 2NVX|1|R, 2NVQ|1|R, 2E2I|1|R, 2E2H|1|R, 1SFO|1|R | (0) | (1) 7OO3|1|P |
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 | 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 | 2NVQ|1|R | RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP | X-RAY DIFFRACTION | 2.9 | 10 |
7 | 2E2I|1|R | RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTP | X-RAY DIFFRACTION | 3.41 | 10 |
8 | 2YU9|1|R | RNA polymerase II elongation complex in 150 mm MG+2 with UTP | X-RAY DIFFRACTION | 3.4 | 10 |
9 | 2NVX|1|R | RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP | X-RAY DIFFRACTION | 3.6 | 10 |
10 | 1SFO|1|R | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX | X-RAY DIFFRACTION | 3.61 | 10 |
11 | 1R9T|1|R | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE | X-RAY DIFFRACTION | 3.5 | 10 |
12 | 1R9S|1|R | RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE | X-RAY DIFFRACTION | 4.25 | 10 |
13 | 6H68|1|R | Yeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD) with fully-ordered A49 | ELECTRON MICROSCOPY | 4.6 | 10 |
14 | 2NVZ|1|R | RNA Polymerase II elongation complex with UTP, updated 11/2006 | X-RAY DIFFRACTION | 4.3 | 10 |
15 | 2E2H|1|R | RNA polymerase II elongation complex at 5 mM Mg2+ with GTP | X-RAY DIFFRACTION | 3.95 | 10 |
16 | 7KEF|1|R | RNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state | X-RAY DIFFRACTION | 3.89 | 10 |
17 | 5VVR|1|R | Ternary complex of RNA Pol II, transcription scaffold and Rad26 | ELECTRON MICROSCOPY | 5.8 | 10 |
18 | 6UPZ|1|R | RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3 | X-RAY DIFFRACTION | 3.1 | 10 |