BGSU RNA Site //

Equivalence class NR_3.0_05529.1 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodÅDate
11XPE|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 SiteX-ray diffraction1.942005-10-18
21XPF|1|A+ 1XPF|1|B5'-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 SiteX-ray diffraction2.32005-10-18
32B8S|1|A+ 2B8S|1|B5'-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 DISX-ray diffraction2.762005-10-25
42B8R|1|A+ 2B8R|1|B5'-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 DISX-ray diffraction2.62005-10-25
51XP7|1|A+ 1XP7|1|B5'-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 SiteX-ray diffraction2.52005-10-18
61Y3O|1|A+ 1Y3O|1|B5'-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 soakedX-ray diffraction2.72005-11-08
72FCY|1|A+ 2FCY|1|BHIV-1 DIS RNAHIV-1 DIS kissing-loop in complex with NeomycinX-ray diffraction2.22006-05-16
81ZCI|1|A+ 1ZCI|1|B5'-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 formX-ray diffraction1.652006-01-31
92FCX|1|A+ 2FCX|1|BHIV-1 DIS RNAHIV-1 DIS kissing-loop in complex with neamineX-ray diffraction22006-05-16
101Y3S|1|A+ 1Y3S|1|B5'-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 formX-ray diffraction2.252005-11-08
112FCZ|1|A+ 2FCZ|1|BHIV-1 DIS RNAHIV-1 DIS kissing-loop in complex with ribostamycinX-ray diffraction2.012006-05-16
121YXP|1|A+ 1YXP|1|B5'-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 soakedX-ray diffraction2.42006-01-31
132FD0|1|A+ 2FD0|1|BHIV-1 DIS RNAHIV-1 DIS kissing-loop in complex with lividomycinX-ray diffraction1.82006-05-16
141ZCI|1|C+ 1ZCI|1|D5'-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 formX-ray diffraction1.652006-01-31
152FCZ|1|C+ 2FCZ|1|DHIV-1 DIS RNAHIV-1 DIS kissing-loop in complex with ribostamycinX-ray diffraction2.012006-05-16
161Y99|1|A+ 1Y99|1|B5'-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 duplexX-ray diffraction2.42004-12-21
171O3Z|1|B+ 1O3Z|1|AHIV-1 DIS(MAL) GENOMIC RNAHIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKEDX-ray diffraction2.652003-05-27
181Y73|1|B+ 1Y73|1|A5'-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-SoakedX-ray diffraction2.92004-12-21
191Y95|1|B+ 1Y95|1|A5'-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-SoakedX-ray diffraction2.82004-12-21
201Y6T|1|B+ 1Y6T|1|A5'-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-SoakedX-ray diffraction2.62004-12-21
211NLC|1|B+ 1NLC|1|AHIV-1 DIS(MAL) genomic RNAHIV-1 DIS(Mal) duplex Zn-soakedX-ray diffraction1.852003-05-13
221Y6S|1|B+ 1Y6S|1|A5'-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-soakedX-ray diffraction2.92004-12-21
231WVD|1|B+ 1WVD|1|A5'-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-SoakedX-ray diffraction2.932004-12-21
24462D|1|B+ 462D|1|ARNA (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 SITEX-ray diffraction2.31999-12-02
252OIY|1|A+ 2OIY|1|B5'-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 siteX-ray diffraction1.62007-12-25
262OIJ|1|A+ 2OIJ|1|B5'-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 soakedX-ray diffraction2.312007-02-13
272OJ0|1|A+ 2OJ0|1|B5'-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 soakedX-ray diffraction2.62007-12-25
283C44|1|A+ 3C44|1|BHIV-1 subtype F genomic RNACrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycinX-ray diffraction22008-05-06
292QEK|1|A+ 2QEK|1|BHIV-1 subtype F DIS genomic RNAHIV-1 subtype F DIS RNA extended duplex formX-ray diffraction1.82008-05-06
303FAR|1|A+ 3FAR|1|BRNA (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 SiteX-ray diffraction2.42009-11-24
313DVV|1|A+ 3DVV|1|BHIV-1 genomic RNACrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)X-ray diffraction22008-08-12

Release history

Release2.02.12.22.32.42.52.62.72.82.92.102.112.122.132.142.152.162.172.182.192.202.212.222.232.242.252.262.272.282.292.302.312.322.332.342.352.362.372.382.392.402.412.422.432.442.452.462.472.482.492.502.512.522.532.542.552.562.572.582.592.602.612.622.632.642.652.662.672.682.692.702.712.722.732.742.752.762.772.782.792.802.812.822.832.842.852.862.872.882.892.902.912.92
Date2014-12-052014-12-122014-12-192014-12-262015-01-022015-01-092015-01-162015-01-232015-01-302015-02-062015-02-132015-02-202015-02-272015-03-062015-03-132015-03-202015-03-272015-04-032015-04-102015-04-172015-04-242015-05-012015-05-082015-05-152015-05-222015-05-292015-06-052015-06-122015-06-192015-06-262015-07-032015-07-102015-07-172015-07-242015-07-312015-08-072015-08-142015-08-212015-08-282015-09-042015-09-112015-09-182015-09-252015-10-022015-10-092015-10-162015-10-232015-10-302015-11-062015-11-132015-11-202015-11-272015-12-042015-12-112015-12-182015-12-252016-01-012016-01-082016-01-152016-01-222016-01-292016-02-052016-02-122016-02-192016-02-262016-03-042016-03-112016-03-182016-03-252016-04-012016-04-082016-04-152016-04-222016-04-292016-05-062016-05-132016-05-202016-05-272016-06-032016-06-102016-06-172016-06-242016-07-012016-07-082016-07-152016-07-222016-07-292016-08-052016-08-122016-08-192016-08-262016-09-022016-09-09

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_3.0_05529.1NR_3.0_60167.12.93(16) 2OJ0|1|A+2OJ0|1|B, 1Y6S|1|B+1Y6S|1|A, 2QEK|1|A+2QEK|1|B, 1Y6T|1|B+1Y6T|1|A, 3C44|1|A+3C44|1|B, 1Y73|1|B+1Y73|1|A, 1Y99|1|A+1Y99|1|B, 1NLC|1|B+1NLC|1|A, 3DVV|1|A+3DVV|1|B, 2OIJ|1|A+2OIJ|1|B, 1O3Z|1|B+1O3Z|1|A, 3FAR|1|A+3FAR|1|B, 2OIY|1|A+2OIY|1|B, 1WVD|1|B+1WVD|1|A, 1Y95|1|B+1Y95|1|A, 462D|1|B+462D|1|A(15) 1Y3O|1|A+1Y3O|1|B, 2FCZ|1|A+2FCZ|1|B, 1Y3S|1|A+1Y3S|1|B, 2FCZ|1|C+2FCZ|1|D, 1YXP|1|A+1YXP|1|B, 2FD0|1|A+2FD0|1|B, 1XP7|1|A+1XP7|1|B, 2B8S|1|A+2B8S|1|B, 1XPE|1|A+1XPE|1|B, 2FCX|1|A+2FCX|1|B, 1XPF|1|A+1XPF|1|B, 2FCY|1|A+2FCY|1|B, 1ZCI|1|A+1ZCI|1|B, 1ZCI|1|C+1ZCI|1|D, 2B8R|1|A+2B8R|1|B(0)
NR_3.0_05529.1NR_3.0_78706.12.93(15) 1XP7|1|A+1XP7|1|B, 1ZCI|1|C+1ZCI|1|D, 2FCZ|1|C+2FCZ|1|D, 1XPE|1|A+1XPE|1|B, 2B8R|1|A+2B8R|1|B, 2FD0|1|A+2FD0|1|B, 1XPF|1|A+1XPF|1|B, 2B8S|1|A+2B8S|1|B, 1Y3O|1|A+1Y3O|1|B, 1Y3S|1|A+1Y3S|1|B, 2FCX|1|A+2FCX|1|B, 1YXP|1|A+1YXP|1|B, 2FCY|1|A+2FCY|1|B, 1ZCI|1|A+1ZCI|1|B, 2FCZ|1|A+2FCZ|1|B(16) 1NLC|1|B+1NLC|1|A, 1Y99|1|A+1Y99|1|B, 2OIY|1|A+2OIY|1|B, 1WVD|1|B+1WVD|1|A, 2QEK|1|A+2QEK|1|B, 1Y6T|1|B+1Y6T|1|A, 3DVV|1|A+3DVV|1|B, 1Y95|1|B+1Y95|1|A, 462D|1|B+462D|1|A, 2OIJ|1|A+2OIJ|1|B, 1O3Z|1|B+1O3Z|1|A, 2OJ0|1|A+2OJ0|1|B, 1Y6S|1|B+1Y6S|1|A, 3C44|1|A+3C44|1|B, 1Y73|1|B+1Y73|1|A, 3FAR|1|A+3FAR|1|B(0)

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).
#SPDBTitleMethodResolutionLength
12FCZ|1|A+2FCZ|1|BHIV-1 DIS kissing-loop in complex with ribostamycinX-RAY DIFFRACTION2.0122
22FD0|1|A+2FD0|1|BHIV-1 DIS kissing-loop in complex with lividomycinX-RAY DIFFRACTION1.822
32FCY|1|A+2FCY|1|BHIV-1 DIS kissing-loop in complex with NeomycinX-RAY DIFFRACTION2.222
42FCZ|1|C+2FCZ|1|DHIV-1 DIS kissing-loop in complex with ribostamycinX-RAY DIFFRACTION2.0122
52FCX|1|A+2FCX|1|BHIV-1 DIS kissing-loop in complex with neamineX-RAY DIFFRACTION222
62B8R|1|A+2B8R|1|BStructure oF HIV-1(LAI) genomic RNA DISX-RAY DIFFRACTION2.623
71XPE|1|A+1XPE|1|BHIV-1 subtype B genomic RNA Dimerization Initiation SiteX-RAY DIFFRACTION1.9423
82B8S|1|A+2B8S|1|BStructure of HIV-1(MAL) genomic RNA DISX-RAY DIFFRACTION2.7623
91XP7|1|A+1XP7|1|BHIV-1 subtype F genomic RNA Dimerization Initiation SiteX-RAY DIFFRACTION2.523
101Y3O|1|A+1Y3O|1|BHIV-1 DIS RNA subtype F- Mn soakedX-RAY DIFFRACTION2.722
111Y3S|1|A+1Y3S|1|BHIV-1 DIS RNA subtype F- MPD formX-RAY DIFFRACTION2.2522
121YXP|1|A+1YXP|1|BHIV-1 DIS RNA subtype F- Zn soakedX-RAY DIFFRACTION2.422
131XPF|1|A+1XPF|1|BHIV-1 subtype A genomic RNA Dimerization Initiation SiteX-RAY DIFFRACTION2.323
141ZCI|1|C+1ZCI|1|DHIV-1 DIS RNA subtype F- monoclinic formX-RAY DIFFRACTION1.6522
151ZCI|1|A+1ZCI|1|BHIV-1 DIS RNA subtype F- monoclinic formX-RAY DIFFRACTION1.6522
163DVV|1|A+3DVV|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)X-RAY DIFFRACTION222
173C44|1|A+3C44|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycinX-RAY DIFFRACTION223
183FAR|1|A+3FAR|1|BCation-dependent self-cleavage activity in the duplex form of the subtype-B HIV-1 RNA Dimerization Initiation SiteX-RAY DIFFRACTION2.423
192OIY|1|A+2OIY|1|BCrystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation siteX-RAY DIFFRACTION1.623
202OIJ|1|A+2OIJ|1|BHIV-1 subtype B DIS RNA extended duplex AuCl3 soakedX-RAY DIFFRACTION2.3123
212OJ0|1|A+2OJ0|1|BCrystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soakedX-RAY DIFFRACTION2.623
221Y99|1|A+1Y99|1|BHIV-1 subtype A DIS RNA duplexX-RAY DIFFRACTION2.426
231Y6S|1|B+1Y6S|1|AHIV-1 DIS(Mal) duplex Ba-soakedX-RAY DIFFRACTION2.926
241Y6T|1|B+1Y6T|1|AHIV-1 Dis(Mal) Duplex Co Hexamine-SoakedX-RAY DIFFRACTION2.626
251Y73|1|B+1Y73|1|AHIV-1 Dis(Mal) Duplex Pt-SoakedX-RAY DIFFRACTION2.926
261Y95|1|B+1Y95|1|AHIV-1 Dis(Mal) Duplex Pb-SoakedX-RAY DIFFRACTION2.826
27462D|1|B+462D|1|ACRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITEX-RAY DIFFRACTION2.326
281O3Z|1|B+1O3Z|1|AHIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKEDX-RAY DIFFRACTION2.6526
291NLC|1|B+1NLC|1|AHIV-1 DIS(Mal) duplex Zn-soakedX-RAY DIFFRACTION1.8526
301WVD|1|B+1WVD|1|AHIV-1 Dis(Mal) Duplex CoCl2-SoakedX-RAY DIFFRACTION2.9326
312QEK|1|A+2QEK|1|BHIV-1 subtype F DIS RNA extended duplex formX-RAY DIFFRACTION1.823
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