BGSU RNA Site

Equivalence class NR_4.0_60167.4 Current

#PDBTitleRNA source organismCompoundsMethodResolutionDate
13C3Z|1|A+3C3Z|1|B (rep)Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycinHIV-1 subtype F genomic RNA, HIV-1 subtype F genomic RNAX-RAY DIFFRACTION1.52008-05-06
21Y99|1|A+1Y99|1|BHIV-1 subtype A DIS RNA duplex5'-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', 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'X-RAY DIFFRACTION2.42004-12-21
31O3Z|1|B+1O3Z|1|AHIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKEDHIV-1 DIS(MAL) GENOMIC RNA, HIV-1 DIS(MAL) GENOMIC RNAX-RAY DIFFRACTION2.652003-05-27
41Y73|1|B+1Y73|1|AHIV-1 Dis(Mal) Duplex Pt-Soaked5'-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', 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'X-RAY DIFFRACTION2.92004-12-21
51Y95|1|B+1Y95|1|AHIV-1 Dis(Mal) Duplex Pb-Soaked5'-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', 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'X-RAY DIFFRACTION2.82004-12-21
61Y6T|1|B+1Y6T|1|AHIV-1 Dis(Mal) Duplex Co Hexamine-Soaked5'-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', 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'X-RAY DIFFRACTION2.62004-12-21
71NLC|1|B+1NLC|1|AHIV-1 DIS(Mal) duplex Zn-soakedHIV-1 DIS(MAL) genomic RNA, HIV-1 DIS(MAL) genomic RNAX-RAY DIFFRACTION1.852003-05-13
81WVD|1|B+1WVD|1|AHIV-1 Dis(Mal) Duplex CoCl2-Soaked5'-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', 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'X-RAY DIFFRACTION2.932004-12-21
91Y6S|1|B+1Y6S|1|AHIV-1 DIS(Mal) duplex Ba-soaked5'-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', 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'X-RAY DIFFRACTION2.92004-12-21
10462D|1|B+462D|1|ACRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITERNA (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'), 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')X-RAY DIFFRACTION2.31999-12-02
111Y90|1|B+1Y90|1|AHIV-1 Dis(Mal) Duplex Mn-Soaked5'-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', 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'X-RAY DIFFRACTION3.082004-12-21
122OIJ|1|A+2OIJ|1|BHIV-1 subtype B DIS RNA extended duplex AuCl3 soaked5'-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', 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'X-RAY DIFFRACTION2.312007-02-13
132QEK|1|A+2QEK|1|BHIV-1 subtype F DIS RNA extended duplex formHIV-1 subtype F DIS genomic RNA, HIV-1 subtype F DIS genomic RNAX-RAY DIFFRACTION1.82008-05-06
143FAR|1|A+3FAR|1|BCation-dependent self-cleavage activity in the duplex form of the subtype-B HIV-1 RNA Dimerization Initiation SiteRNA (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'), 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')X-RAY DIFFRACTION2.42009-11-24
152OJ0|1|A+2OJ0|1|BCrystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked5'-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', 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'X-RAY DIFFRACTION2.62007-12-25
162OIY|1|A+2OIY|1|BCrystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site5'-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', 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'X-RAY DIFFRACTION1.62007-12-25
173C44|1|A+3C44|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycinHIV-1 subtype F genomic RNA, HIV-1 subtype F genomic RNAX-RAY DIFFRACTION22008-05-06
183DVV|1|A+3DVV|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)HIV-1 genomic RNA, HIV-1 genomic RNAX-RAY DIFFRACTION22008-08-12
193C7R|1|A+3C7R|1|BCrystal Structure of HIV-1 subtype F DIS extended duplex RNA bound to neomycinHIV-1 subtype F genomic RNA, HIV-1 subtype F genomic RNAX-RAY DIFFRACTION1.72008-05-06
203C5D|1|A+3C5D|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin'HIV-1 subtype F genomic RNA, 'HIV-1 subtype F genomic RNAX-RAY DIFFRACTION1.82008-05-06

Release history

Release2.1532.1542.1552.1562.1572.1583.03.13.23.33.43.53.63.73.83.93.103.11
Date2017-11-032017-11-102017-11-172017-11-242017-12-012017-12-082017-12-152017-12-222017-12-292018-01-052018-01-122018-01-192018-01-262018-02-022018-02-092018-02-162018-02-232018-03-01

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_4.0_60167.4NR_4.0_60167.32.153(17) 3C44|1|A+3C44|1|B, 1WVD|1|B+1WVD|1|A, 2QEK|1|A+2QEK|1|B, 1O3Z|1|B+1O3Z|1|A, 2OJ0|1|A+2OJ0|1|B, 1NLC|1|B+1NLC|1|A, 2OIY|1|A+2OIY|1|B, 2OIJ|1|A+2OIJ|1|B, 1Y99|1|A+1Y99|1|B, 1Y95|1|B+1Y95|1|A, 1Y90|1|B+1Y90|1|A, 462D|1|B+462D|1|A, 1Y73|1|B+1Y73|1|A, 3FAR|1|A+3FAR|1|B, 1Y6T|1|B+1Y6T|1|A, 3DVV|1|A+3DVV|1|B, 1Y6S|1|B+1Y6S|1|A(3) 3C5D|1|A+3C5D|1|B, 3C7R|1|A+3C7R|1|B, 3C3Z|1|A+3C3Z|1|B(0)

Children

This classDescendant classesRelease idIntersectionOnly in this classAdded to child

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
12QEK|1|A+2QEK|1|BHIV-1 subtype F DIS RNA extended duplex formX-RAY DIFFRACTION1.823
21Y90|1|B+1Y90|1|AHIV-1 Dis(Mal) Duplex Mn-SoakedX-RAY DIFFRACTION3.0825
31WVD|1|B+1WVD|1|AHIV-1 Dis(Mal) Duplex CoCl2-SoakedX-RAY DIFFRACTION2.9326
41NLC|1|B+1NLC|1|AHIV-1 DIS(Mal) duplex Zn-soakedX-RAY DIFFRACTION1.8526
51O3Z|1|B+1O3Z|1|AHIV-1 DIS(MAL) DUPLEX RU HEXAMINE-SOAKEDX-RAY DIFFRACTION2.6526
6462D|1|B+462D|1|ACRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITEX-RAY DIFFRACTION2.326
71Y95|1|B+1Y95|1|AHIV-1 Dis(Mal) Duplex Pb-SoakedX-RAY DIFFRACTION2.826
81Y73|1|B+1Y73|1|AHIV-1 Dis(Mal) Duplex Pt-SoakedX-RAY DIFFRACTION2.926
91Y6T|1|B+1Y6T|1|AHIV-1 Dis(Mal) Duplex Co Hexamine-SoakedX-RAY DIFFRACTION2.626
101Y6S|1|B+1Y6S|1|AHIV-1 DIS(Mal) duplex Ba-soakedX-RAY DIFFRACTION2.926
111Y99|1|A+1Y99|1|BHIV-1 subtype A DIS RNA duplexX-RAY DIFFRACTION2.426
122OJ0|1|A+2OJ0|1|BCrystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soakedX-RAY DIFFRACTION2.623
133FAR|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
142OIY|1|A+2OIY|1|BCrystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation siteX-RAY DIFFRACTION1.623
152OIJ|1|A+2OIJ|1|BHIV-1 subtype B DIS RNA extended duplex AuCl3 soakedX-RAY DIFFRACTION2.3123
163C44|1|A+3C44|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycinX-RAY DIFFRACTION223
173C5D|1|A+3C5D|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycinX-RAY DIFFRACTION1.822
183C7R|1|A+3C7R|1|BCrystal Structure of HIV-1 subtype F DIS extended duplex RNA bound to neomycinX-RAY DIFFRACTION1.722
193C3Z|1|A+3C3Z|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycinX-RAY DIFFRACTION1.522
203DVV|1|A+3DVV|1|BCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)X-RAY DIFFRACTION222