Equivalence class NR_3.5_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 | 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 | 1Y90|1|B+ 1Y90|1|A | 5'-R(*CP*(5BU)P*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 Mn-Soaked | X-ray diffraction | 3.08 | 2004-12-21 | ||||
| 12 | 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 | ||||
| 13 | 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 | ||||
| 14 | 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 | ||||
| 15 | 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 | ||||
| 16 | 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 | ||||
| 17 | 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_3.5_60167.1 | NR_3.5_05529.1 | 2.93 | (17) 1NLC|1|B+1NLC|1|A, 1O3Z|1|B+1O3Z|1|A, 1WVD|1|B+1WVD|1|A, 1Y6S|1|B+1Y6S|1|A, 1Y6T|1|B+1Y6T|1|A, 1Y73|1|B+1Y73|1|A, 1Y90|1|B+1Y90|1|A, 1Y95|1|B+1Y95|1|A, 1Y99|1|A+1Y99|1|B, 2OIJ|1|A+2OIJ|1|B, 2OIY|1|A+2OIY|1|B, 2OJ0|1|A+2OJ0|1|B, 2QEK|1|A+2QEK|1|B, 3C44|1|A+3C44|1|B, 3DVV|1|A+3DVV|1|B, 3FAR|1|A+3FAR|1|B, 462D|1|B+462D|1|A | (0) | (17) 1K9W|1|B, 1K9W|1|D, 1XP7|1|A+1XP7|1|B, 1XPE|1|A+1XPE|1|B, 1XPF|1|A+1XPF|1|B, 1Y3O|1|A+1Y3O|1|B, 1Y3S|1|A+1Y3S|1|B, 1YXP|1|A+1YXP|1|B, 1ZCI|1|A+1ZCI|1|B, 1ZCI|1|C+1ZCI|1|D, 2B8R|1|A+2B8R|1|B, 2B8S|1|A+2B8S|1|B, 2FCX|1|A+2FCX|1|B, 2FCY|1|A+2FCY|1|B, 2FCZ|1|A+2FCZ|1|B, 2FCZ|1|C+2FCZ|1|D, 2FD0|1|A+2FD0|1|B |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_60167.1 | NR_3.5_60167.2 | 2.124 | (17) 1NLC|1|B+1NLC|1|A, 1O3Z|1|B+1O3Z|1|A, 1WVD|1|B+1WVD|1|A, 1Y6S|1|B+1Y6S|1|A, 1Y6T|1|B+1Y6T|1|A, 1Y73|1|B+1Y73|1|A, 1Y90|1|B+1Y90|1|A, 1Y95|1|B+1Y95|1|A, 1Y99|1|A+1Y99|1|B, 2OIJ|1|A+2OIJ|1|B, 2OIY|1|A+2OIY|1|B, 2OJ0|1|A+2OJ0|1|B, 2QEK|1|A+2QEK|1|B, 3C44|1|A+3C44|1|B, 3DVV|1|A+3DVV|1|B, 3FAR|1|A+3FAR|1|B, 462D|1|B+462D|1|A | (0) | (3) 3C3Z|1|A+3C3Z|1|B, 3C5D|1|A+3C5D|1|B, 3C7R|1|A+3C7R|1|B |
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.
| #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 | 1Y90|1|B+1Y90|1|A | HIV-1 Dis(Mal) Duplex Mn-Soaked | X-RAY DIFFRACTION | 3.08 | 25 |
| 3 | 1WVD|1|B+1WVD|1|A | HIV-1 Dis(Mal) Duplex CoCl2-Soaked | X-RAY DIFFRACTION | 2.93 | 26 |
| 4 | 1NLC|1|B+1NLC|1|A | HIV-1 DIS(Mal) duplex Zn-soaked | X-RAY DIFFRACTION | 1.85 | 26 |
| 5 | 1O3Z|1|B+1O3Z|1|A | HIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKED | X-RAY DIFFRACTION | 2.65 | 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 | 1Y95|1|B+1Y95|1|A | HIV-1 Dis(Mal) Duplex Pb-Soaked | X-RAY DIFFRACTION | 2.8 | 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 | 1Y6S|1|B+1Y6S|1|A | HIV-1 DIS(Mal) duplex Ba-soaked | X-RAY DIFFRACTION | 2.9 | 26 |
| 11 | 1Y99|1|A+1Y99|1|B | HIV-1 subtype A DIS RNA duplex | X-RAY DIFFRACTION | 2.4 | 26 |
| 12 | 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 |
| 13 | 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 |
| 14 | 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 |
| 15 | 2OIJ|1|A+2OIJ|1|B | HIV-1 subtype B DIS RNA extended duplex AuCl3 soaked | X-RAY DIFFRACTION | 2.31 | 23 |
| 16 | 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 |
| 17 | 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 |
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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