Equivalence class NR_all_05529.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1XPE|1|A+ 1XPE|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' | HIV-1 subtype B genomic RNA Dimerization Initiation Site | X-ray diffraction | 1.94 | 46 | 2005-10-18 | ||||
| 2 | 1XPF|1|A+ 1XPF|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 genomic RNA Dimerization Initiation Site | X-ray diffraction | 2.3 | 46 | 2005-10-18 | ||||
| 3 | 2B8S|1|A+ 2B8S|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' | Structure of HIV-1(MAL) genomic RNA DIS | X-ray diffraction | 2.76 | 46 | 2005-10-25 | ||||
| 4 | 2B8R|1|A+ 2B8R|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' | Structure oF HIV-1(LAI) genomic RNA DIS | X-ray diffraction | 2.6 | 46 | 2005-10-25 | ||||
| 5 | 1XP7|1|A+ 1XP7|1|B | 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 subtype F genomic RNA Dimerization Initiation Site | X-ray diffraction | 2.5 | 46 | 2005-10-18 | ||||
| 6 | 1JTJ|1|A | HIV-1Lai SL1 | Solution structure of HIV-1Lai mutated SL1 hairpin | Solution NMR | 23 | 2002-12-11 | |||||
| 7 | 1Y3O|1|A+ 1Y3O|1|B | 5'-R(*CP*UP*(5BU)P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- Mn soaked | X-ray diffraction | 2.7 | 46 | 2005-11-08 | ||||
| 8 | 2FCY|1|A+ 2FCY|1|B | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with Neomycin | X-ray diffraction | 2.2 | 46 | 2006-05-16 | ||||
| 9 | 1ZCI|1|A+ 1ZCI|1|B | 5'-R(*CP*(5BU)P*UP*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- monoclinic form | X-ray diffraction | 1.65 | 46 | 2006-01-31 | ||||
| 10 | 2FCX|1|A+ 2FCX|1|B | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with neamine | X-ray diffraction | 2 | 46 | 2006-05-16 | ||||
| 11 | 1Y3S|1|A+ 1Y3S|1|B | 5'-R(*CP*UP*(5BU)P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- MPD form | X-ray diffraction | 2.25 | 46 | 2005-11-08 | ||||
| 12 | 2FCZ|1|A+ 2FCZ|1|B | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with ribostamycin | X-ray diffraction | 2.01 | 46 | 2006-05-16 | ||||
| 13 | 1YXP|1|A+ 1YXP|1|B | 5'-R(*CP*UP*(5BU)P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- Zn soaked | X-ray diffraction | 2.4 | 46 | 2006-01-31 | ||||
| 14 | 2FD0|1|A+ 2FD0|1|B | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with lividomycin | X-ray diffraction | 1.8 | 46 | 2006-05-16 | ||||
| 15 | 1ZCI|1|C+ 1ZCI|1|D | 5'-R(*CP*(5BU)P*UP*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' | HIV-1 DIS RNA subtype F- monoclinic form | X-ray diffraction | 1.65 | 46 | 2006-01-31 | ||||
| 16 | 2FCZ|1|C+ 2FCZ|1|D | HIV-1 DIS RNA | HIV-1 DIS kissing-loop in complex with ribostamycin | X-ray diffraction | 2.01 | 46 | 2006-05-16 | ||||
| 17 | 1K9W|1|B | HIV-1 DIS(Mal)UU RNA | HIV-1(MAL) RNA Dimerization Initiation Site | X-ray diffraction | 3.1 | 23 | 2001-11-30 | ||||
| 18 | 1K9W|1|D | HIV-1 DIS(Mal)UU RNA | HIV-1(MAL) RNA Dimerization Initiation Site | X-ray diffraction | 3.1 | 23 | 2001-11-30 | ||||
| 19 | 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 | 46 | 2004-12-21 | ||||
| 20 | 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 | 23 | 2003-05-27 | ||||
| 21 | 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 | 23 | 2004-12-21 | ||||
| 22 | 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 | 23 | 2004-12-21 | ||||
| 23 | 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 | 23 | 2004-12-21 | ||||
| 24 | 1NLC|1|B+ 1NLC|1|A | HIV-1 DIS(MAL) genomic RNA | HIV-1 DIS(Mal) duplex Zn-soaked | X-ray diffraction | 1.85 | 23 | 2003-05-13 | ||||
| 25 | 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 | 23 | 2004-12-21 | ||||
| 26 | 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 | 23 | 2004-12-21 | ||||
| 27 | 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 | 23 | 1999-12-02 | ||||
| 28 | 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 | 22 | 2004-12-21 | ||||
| 29 | 1JU1|1|A+ 1JU1|1|B | HIV-1Lai SL1 | Dimer Initiation Sequence of HIV-1Lai Genomic RNA: NMR Solution Structure of the Extended Duplex | Solution NMR | 23 | 2002-08-23 | |||||
| 30 | 2OIY|1|A+ 2OIY|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 | X-ray diffraction | 1.6 | 46 | 2007-12-25 | ||||
| 31 | 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 | 46 | 2007-02-13 | ||||
| 32 | 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 | 46 | 2007-12-25 | ||||
| 33 | 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 | 46 | 2008-05-06 | ||||
| 34 | 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 | 46 | 2008-05-06 | ||||
| 35 | 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 | 46 | 2009-11-24 | ||||
| 36 | 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 | 46 | 2008-08-12 |
Release history
| Release | 2.0 | 2.1 | 2.2 | 2.3 | 2.4 | 2.5 | 2.6 | 2.7 | 2.8 | 2.9 | 2.10 | 2.11 | 2.12 | 2.13 | 2.14 | 2.15 | 2.16 | 2.17 | 2.18 | 2.19 | 2.20 | 2.21 | 2.22 | 2.23 | 2.24 | 2.25 | 2.26 | 2.27 | 2.28 | 2.29 | 2.30 | 2.31 | 2.32 | 2.33 | 2.34 | 2.35 | 2.36 | 2.37 | 2.38 | 2.39 | 2.40 | 2.41 | 2.42 | 2.43 | 2.44 | 2.45 | 2.46 | 2.47 | 2.48 | 2.49 | 2.50 | 2.51 | 2.52 | 2.53 | 2.54 | 2.55 | 2.56 | 2.57 | 2.58 | 2.59 | 2.60 | 2.61 | 2.62 | 2.63 | 2.64 | 2.65 | 2.66 | 2.67 | 2.68 | 2.69 | 2.70 | 2.71 | 2.72 | 2.73 | 2.74 | 2.75 | 2.76 | 2.77 | 2.78 | 2.79 | 2.80 | 2.81 | 2.82 | 2.83 | 2.84 | 2.85 | 2.86 | 2.87 | 2.88 | 2.89 | 2.90 | 2.91 | 2.92 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2014-12-05 | 2014-12-12 | 2014-12-19 | 2014-12-26 | 2015-01-02 | 2015-01-09 | 2015-01-16 | 2015-01-23 | 2015-01-30 | 2015-02-06 | 2015-02-13 | 2015-02-20 | 2015-02-27 | 2015-03-06 | 2015-03-13 | 2015-03-20 | 2015-03-27 | 2015-04-03 | 2015-04-10 | 2015-04-17 | 2015-04-24 | 2015-05-01 | 2015-05-08 | 2015-05-15 | 2015-05-22 | 2015-05-29 | 2015-06-05 | 2015-06-12 | 2015-06-19 | 2015-06-26 | 2015-07-03 | 2015-07-10 | 2015-07-17 | 2015-07-24 | 2015-07-31 | 2015-08-07 | 2015-08-14 | 2015-08-21 | 2015-08-28 | 2015-09-04 | 2015-09-11 | 2015-09-18 | 2015-09-25 | 2015-10-02 | 2015-10-09 | 2015-10-16 | 2015-10-23 | 2015-10-30 | 2015-11-06 | 2015-11-13 | 2015-11-20 | 2015-11-27 | 2015-12-04 | 2015-12-11 | 2015-12-18 | 2015-12-25 | 2016-01-01 | 2016-01-08 | 2016-01-15 | 2016-01-22 | 2016-01-29 | 2016-02-05 | 2016-02-12 | 2016-02-19 | 2016-02-26 | 2016-03-04 | 2016-03-11 | 2016-03-18 | 2016-03-25 | 2016-04-01 | 2016-04-08 | 2016-04-15 | 2016-04-22 | 2016-04-29 | 2016-05-06 | 2016-05-13 | 2016-05-20 | 2016-05-27 | 2016-06-03 | 2016-06-10 | 2016-06-17 | 2016-06-24 | 2016-07-01 | 2016-07-08 | 2016-07-15 | 2016-07-22 | 2016-07-29 | 2016-08-05 | 2016-08-12 | 2016-08-19 | 2016-08-26 | 2016-09-02 | 2016-09-09 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
Children
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 | 1JU1|1|A+ 1JU1|1|B | Dimer Initiation Sequence of HIV-1Lai Genomic RNA: NMR Solution Structure of the Extended Duplex | SOLUTION NMR | 23 | ||
| 2 | 2QEK|1|A+ 2QEK|1|B | HIV-1 subtype F DIS RNA extended duplex form | X-RAY DIFFRACTION | 1.8 | 46 | |
| 3 | 1Y6S|1|B+ 1Y6S|1|A | HIV-1 DIS(Mal) duplex Ba-soaked | X-RAY DIFFRACTION | 2.9 | 23 | |
| 4 | 1Y95|1|B+ 1Y95|1|A | HIV-1 Dis(Mal) Duplex Pb-Soaked | X-RAY DIFFRACTION | 2.8 | 23 | |
| 5 | 1Y90|1|B+ 1Y90|1|A | HIV-1 Dis(Mal) Duplex Mn-Soaked | X-RAY DIFFRACTION | 3.08 | 22 | |
| 6 | 1WVD|1|B+ 1WVD|1|A | HIV-1 Dis(Mal) Duplex CoCl2-Soaked | X-RAY DIFFRACTION | 2.93 | 23 | |
| 7 | 1NLC|1|B+ 1NLC|1|A | HIV-1 DIS(Mal) duplex Zn-soaked | X-RAY DIFFRACTION | 1.85 | 23 | |
| 8 | 462D|1|B+ 462D|1|A | CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE | X-RAY DIFFRACTION | 2.3 | 23 | |
| 9 | 1O3Z|1|B+ 1O3Z|1|A | HIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKED | X-RAY DIFFRACTION | 2.65 | 23 | |
| 10 | 1Y73|1|B+ 1Y73|1|A | HIV-1 Dis(Mal) Duplex Pt-Soaked | X-RAY DIFFRACTION | 2.9 | 23 | |
| 11 | 1Y6T|1|B+ 1Y6T|1|A | HIV-1 Dis(Mal) Duplex Co Hexamine-Soaked | X-RAY DIFFRACTION | 2.6 | 23 | |
| 12 | 1Y99|1|A+ 1Y99|1|B | HIV-1 subtype A DIS RNA duplex | X-RAY DIFFRACTION | 2.4 | 46 | |
| 13 | 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 | 46 | |
| 14 | 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 | 46 | |
| 15 | 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 | 46 | |
| 16 | 2OIJ|1|A+ 2OIJ|1|B | HIV-1 subtype B DIS RNA extended duplex AuCl3 soaked | X-RAY DIFFRACTION | 2.31 | 46 | |
| 17 | 3C44|1|A+ 3C44|1|B | Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin | X-RAY DIFFRACTION | 2 | 46 | |
| 18 | 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 | 46 | |
| 19 | 1ZCI|1|C+ 1ZCI|1|D | HIV-1 DIS RNA subtype F- monoclinic form | X-RAY DIFFRACTION | 1.65 | 46 | |
| 20 | 1ZCI|1|A+ 1ZCI|1|B | HIV-1 DIS RNA subtype F- monoclinic form | X-RAY DIFFRACTION | 1.65 | 46 | |
| 21 | 1XPE|1|A+ 1XPE|1|B | HIV-1 subtype B genomic RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 1.94 | 46 | |
| 22 | 2B8R|1|A+ 2B8R|1|B | Structure oF HIV-1(LAI) genomic RNA DIS | X-RAY DIFFRACTION | 2.6 | 46 | |
| 23 | 2B8S|1|A+ 2B8S|1|B | Structure of HIV-1(MAL) genomic RNA DIS | X-RAY DIFFRACTION | 2.76 | 46 | |
| 24 | 1XP7|1|A+ 1XP7|1|B | HIV-1 subtype F genomic RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 2.5 | 46 | |
| 25 | 1Y3O|1|A+ 1Y3O|1|B | HIV-1 DIS RNA subtype F- Mn soaked | X-RAY DIFFRACTION | 2.7 | 46 | |
| 26 | 1Y3S|1|A+ 1Y3S|1|B | HIV-1 DIS RNA subtype F- MPD form | X-RAY DIFFRACTION | 2.25 | 46 | |
| 27 | 1YXP|1|A+ 1YXP|1|B | HIV-1 DIS RNA subtype F- Zn soaked | X-RAY DIFFRACTION | 2.4 | 46 | |
| 28 | 1XPF|1|A+ 1XPF|1|B | HIV-1 subtype A genomic RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 2.3 | 46 | |
| 29 | 1K9W|1|B | HIV-1(MAL) RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 3.1 | 23 | |
| 30 | 1K9W|1|D | HIV-1(MAL) RNA Dimerization Initiation Site | X-RAY DIFFRACTION | 3.1 | 23 | |
| 31 | 2FCX|1|A+ 2FCX|1|B | HIV-1 DIS kissing-loop in complex with neamine | X-RAY DIFFRACTION | 2 | 46 | |
| 32 | 2FCZ|1|C+ 2FCZ|1|D | HIV-1 DIS kissing-loop in complex with ribostamycin | X-RAY DIFFRACTION | 2.01 | 46 | |
| 33 | 2FD0|1|A+ 2FD0|1|B | HIV-1 DIS kissing-loop in complex with lividomycin | X-RAY DIFFRACTION | 1.8 | 46 | |
| 34 | 2FCY|1|A+ 2FCY|1|B | HIV-1 DIS kissing-loop in complex with Neomycin | X-RAY DIFFRACTION | 2.2 | 46 | |
| 35 | 2FCZ|1|A+ 2FCZ|1|B | HIV-1 DIS kissing-loop in complex with ribostamycin | X-RAY DIFFRACTION | 2.01 | 46 | |
| 36 | 1JTJ|1|A | Solution structure of HIV-1Lai mutated SL1 hairpin | SOLUTION NMR | 23 |
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.
Coloring options: