Equivalence class NR_3.0_60167.3 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2OIY|1|A+ 2OIY|1|B (rep) | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3' | Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site | X-ray diffraction | 1.6 | 2007-12-25 | ||||
| 2 | 1Y99|1|A+ 1Y99|1|B | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 subtype A DIS RNA duplex | X-ray diffraction | 2.4 | 2004-12-21 | ||||
| 3 | 1O3Z|1|B+ 1O3Z|1|A | HIV-1 DIS(MAL) GENOMIC RNA | HIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKED | X-ray diffraction | 2.65 | 2003-05-27 | ||||
| 4 | 1Y73|1|B+ 1Y73|1|A | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 Dis(Mal) Duplex Pt-Soaked | X-ray diffraction | 2.9 | 2004-12-21 | ||||
| 5 | 1Y95|1|B+ 1Y95|1|A | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 Dis(Mal) Duplex Pb-Soaked | X-ray diffraction | 2.8 | 2004-12-21 | ||||
| 6 | 462D|1|B+ 462D|1|A | RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G) -3') | CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE | X-ray diffraction | 2.3 | 1999-12-02 | ||||
| 7 | 1NLC|1|B+ 1NLC|1|A | HIV-1 DIS(MAL) genomic RNA | HIV-1 DIS(Mal) duplex Zn-soaked | X-ray diffraction | 1.85 | 2003-05-13 | ||||
| 8 | 1WVD|1|B+ 1WVD|1|A | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 Dis(Mal) Duplex CoCl2-Soaked | X-ray diffraction | 2.93 | 2004-12-21 | ||||
| 9 | 1Y6S|1|B+ 1Y6S|1|A | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS(Mal) duplex Ba-soaked | X-ray diffraction | 2.9 | 2004-12-21 | ||||
| 10 | 1Y6T|1|B+ 1Y6T|1|A | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 Dis(Mal) Duplex Co Hexamine-Soaked | X-ray diffraction | 2.6 | 2004-12-21 | ||||
| 11 | 2OIJ|1|A+ 2OIJ|1|B | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3' | HIV-1 subtype B DIS RNA extended duplex AuCl3 soaked | X-ray diffraction | 2.31 | 2007-02-13 | ||||
| 12 | 2QEK|1|A+ 2QEK|1|B | HIV-1 subtype F DIS genomic RNA | HIV-1 subtype F DIS RNA extended duplex form | X-ray diffraction | 1.8 | 2008-05-06 | ||||
| 13 | 3FAR|1|A+ 3FAR|1|B | RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3') | Cation-dependent self-cleavage activity in the duplex form of the subtype-B HIV-1 RNA Dimerization Initiation Site | X-ray diffraction | 2.4 | 2009-11-24 | ||||
| 14 | 2OJ0|1|A+ 2OJ0|1|B | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3' | Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked | X-ray diffraction | 2.6 | 2007-12-25 | ||||
| 15 | 3C44|1|A+ 3C44|1|B | HIV-1 subtype F genomic RNA | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin | X-ray diffraction | 2 | 2008-05-06 | ||||
| 16 | 3DVV|1|A+ 3DVV|1|B | HIV-1 genomic RNA | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe) | X-ray diffraction | 2 | 2008-08-12 |
Release history
| Release | 2.132 | 2.133 | 2.134 | 2.135 | 2.136 | 2.137 | 2.138 | 2.139 | 2.140 | 2.141 | 2.142 | 2.143 | 2.144 | 2.145 | 2.146 | 2.147 | 2.148 | 2.149 | 2.150 | 2.151 | 2.152 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2017-06-21 | 2017-06-24 | 2017-06-28 | 2017-07-04 | 2017-07-10 | 2017-07-15 | 2017-07-26 | 2017-07-31 | 2017-08-05 | 2017-08-12 | 2017-08-19 | 2017-08-26 | 2017-09-03 | 2017-09-09 | 2017-09-16 | 2017-09-23 | 2017-09-30 | 2017-10-07 | 2017-10-14 | 2017-10-21 | 2017-10-28 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.0_60167.3 | NR_3.0_60167.2 | 2.132 | (16) 1Y73|1|B+1Y73|1|A, 3FAR|1|A+3FAR|1|B, 1Y6S|1|B+1Y6S|1|A, 3C44|1|A+3C44|1|B, 1WVD|1|B+1WVD|1|A, 1NLC|1|B+1NLC|1|A, 2QEK|1|A+2QEK|1|B, 2OIY|1|A+2OIY|1|B, 1Y99|1|A+1Y99|1|B, 1Y95|1|B+1Y95|1|A, 462D|1|B+462D|1|A, 1Y6T|1|B+1Y6T|1|A, 3DVV|1|A+3DVV|1|B, 1O3Z|1|B+1O3Z|1|A, 2OJ0|1|A+2OJ0|1|B, 2OIJ|1|A+2OIJ|1|B | (0) | (3) 3C5D|1|A+3C5D|1|B, 3C7R|1|A+3C7R|1|B, 3C3Z|1|A+3C3Z|1|B |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.0_60167.3 | NR_3.0_60167.4 | 2.153 | (16) 2OJ0|1|A+2OJ0|1|B, 1NLC|1|B+1NLC|1|A, 1Y73|1|B+1Y73|1|A, 462D|1|B+462D|1|A, 1Y6T|1|B+1Y6T|1|A, 2OIY|1|A+2OIY|1|B, 3FAR|1|A+3FAR|1|B, 1Y6S|1|B+1Y6S|1|A, 2OIJ|1|A+2OIJ|1|B, 3DVV|1|A+3DVV|1|B, 1WVD|1|B+1WVD|1|A, 1Y99|1|A+1Y99|1|B, 3C44|1|A+3C44|1|B, 1O3Z|1|B+1O3Z|1|A, 1Y95|1|B+1Y95|1|A, 2QEK|1|A+2QEK|1|B | (0) | (3) 3C7R|1|A+3C7R|1|B, 3C3Z|1|A+3C3Z|1|B, 3C5D|1|A+3C5D|1|B |
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 | 2QEK|1|A+2QEK|1|B | HIV-1 subtype F DIS RNA extended duplex form | X-RAY DIFFRACTION | 1.8 | 23 |
| 2 | 1Y6S|1|B+1Y6S|1|A | HIV-1 DIS(Mal) duplex Ba-soaked | X-RAY DIFFRACTION | 2.9 | 26 |
| 3 | 1Y95|1|B+1Y95|1|A | HIV-1 Dis(Mal) Duplex Pb-Soaked | X-RAY DIFFRACTION | 2.8 | 26 |
| 4 | 1WVD|1|B+1WVD|1|A | HIV-1 Dis(Mal) Duplex CoCl2-Soaked | X-RAY DIFFRACTION | 2.93 | 26 |
| 5 | 1NLC|1|B+1NLC|1|A | HIV-1 DIS(Mal) duplex Zn-soaked | X-RAY DIFFRACTION | 1.85 | 26 |
| 6 | 462D|1|B+462D|1|A | CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE | X-RAY DIFFRACTION | 2.3 | 26 |
| 7 | 1O3Z|1|B+1O3Z|1|A | HIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKED | X-RAY DIFFRACTION | 2.65 | 26 |
| 8 | 1Y73|1|B+1Y73|1|A | HIV-1 Dis(Mal) Duplex Pt-Soaked | X-RAY DIFFRACTION | 2.9 | 26 |
| 9 | 1Y6T|1|B+1Y6T|1|A | HIV-1 Dis(Mal) Duplex Co Hexamine-Soaked | X-RAY DIFFRACTION | 2.6 | 26 |
| 10 | 1Y99|1|A+1Y99|1|B | HIV-1 subtype A DIS RNA duplex | X-RAY DIFFRACTION | 2.4 | 26 |
| 11 | 2OJ0|1|A+2OJ0|1|B | Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked | X-RAY DIFFRACTION | 2.6 | 23 |
| 12 | 3FAR|1|A+3FAR|1|B | Cation-dependent self-cleavage activity in the duplex form of the subtype-B HIV-1 RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 2.4 | 23 |
| 13 | 2OIY|1|A+2OIY|1|B | Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site | X-RAY DIFFRACTION | 1.6 | 23 |
| 14 | 2OIJ|1|A+2OIJ|1|B | HIV-1 subtype B DIS RNA extended duplex AuCl3 soaked | X-RAY DIFFRACTION | 2.31 | 23 |
| 15 | 3C44|1|A+3C44|1|B | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin | X-RAY DIFFRACTION | 2 | 23 |
| 16 | 3DVV|1|A+3DVV|1|B | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe) | X-RAY DIFFRACTION | 2 | 22 |