Equivalence class NR_2.5_60167.1 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 | 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 | ||||
| 4 | 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 | ||||
| 5 | 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 | ||||
| 6 | 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 | ||||
| 7 | 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 | ||||
| 8 | 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 | ||||
| 9 | 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 | 2.93 | 2.94 | 2.95 | 2.96 | 2.97 | 2.98 | 2.99 | 2.100 | 2.101 | 2.102 | 2.103 | 2.104 | 2.105 | 2.106 | 2.107 | 2.108 | 2.109 | 2.110 | 2.111 | 2.112 | 2.113 | 2.114 | 2.115 | 2.116 | 2.117 | 2.118 | 2.119 | 2.120 | 2.121 | 2.122 | 2.123 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2016-09-16 | 2016-09-23 | 2016-09-30 | 2016-10-07 | 2016-10-14 | 2016-10-21 | 2016-10-28 | 2016-11-04 | 2016-11-11 | 2016-11-18 | 2016-11-25 | 2016-12-02 | 2016-12-09 | 2016-12-16 | 2016-12-23 | 2016-12-30 | 2017-01-06 | 2017-01-13 | 2017-01-20 | 2017-01-27 | 2017-02-03 | 2017-02-10 | 2017-02-17 | 2017-02-24 | 2017-03-03 | 2017-03-10 | 2017-03-17 | 2017-03-24 | 2017-03-31 | 2017-04-11 | 2017-04-15 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_60167.1 | NR_2.5_05529.1 | 2.93 | (9) 2OIY|1|A+2OIY|1|B, 3DVV|1|A+3DVV|1|B, 462D|1|B+462D|1|A, 1NLC|1|B+1NLC|1|A, 2OIJ|1|A+2OIJ|1|B, 3C44|1|A+3C44|1|B, 3FAR|1|A+3FAR|1|B, 2QEK|1|A+2QEK|1|B, 1Y99|1|A+1Y99|1|B | (0) | (12) 1YXP|1|A+1YXP|1|B, 1XP7|1|A+1XP7|1|B, 2FCY|1|A+2FCY|1|B, 2FD0|1|A+2FD0|1|B, 2FCX|1|A+2FCX|1|B, 1Y3S|1|A+1Y3S|1|B, 1ZCI|1|C+1ZCI|1|D, 1XPF|1|A+1XPF|1|B, 2FCZ|1|C+2FCZ|1|D, 2FCZ|1|A+2FCZ|1|B, 1ZCI|1|A+1ZCI|1|B, 1XPE|1|A+1XPE|1|B |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_60167.1 | NR_2.5_60167.2 | 2.124 | (9) 2QEK|1|A+2QEK|1|B, 2OIY|1|A+2OIY|1|B, 462D|1|B+462D|1|A, 2OIJ|1|A+2OIJ|1|B, 3FAR|1|A+3FAR|1|B, 1Y99|1|A+1Y99|1|B, 3DVV|1|A+3DVV|1|B, 1NLC|1|B+1NLC|1|A, 3C44|1|A+3C44|1|B | (0) | (3) 3C7R|1|A+3C7R|1|B, 3C5D|1|A+3C5D|1|B, 3C3Z|1|A+3C3Z|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 | 1NLC|1|B+1NLC|1|A | HIV-1 DIS(Mal) duplex Zn-soaked | X-RAY DIFFRACTION | 1.85 | 26 |
| 3 | 462D|1|B+462D|1|A | CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE | X-RAY DIFFRACTION | 2.3 | 26 |
| 4 | 1Y99|1|A+1Y99|1|B | HIV-1 subtype A DIS RNA duplex | X-RAY DIFFRACTION | 2.4 | 26 |
| 5 | 2OIJ|1|A+2OIJ|1|B | HIV-1 subtype B DIS RNA extended duplex AuCl3 soaked | X-RAY DIFFRACTION | 2.31 | 23 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |