BGSU RNA Site //

Equivalence class NR_all_74924.2 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodÅDate
13PF5|1|R (rep)hexaribouracil (rU6)Crystal structure of Bs-CspB in complex with rU6X-ray diffraction1.682011-09-21
25ELX|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Saccharomyces cerevisiaeEukaryaS. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3X-ray diffraction1.812016-02-24
33PEW|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3X-ray diffraction1.52011-03-23
43PEY|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')S. cerevisiae Dbp5 bound to RNA and ADP BeF3X-ray diffraction1.42011-03-23
54ALP|1|EHEXA URIDINEsynthetic constructSyntheticThe Lin28b Cold shock domain in complex with hexauridineX-ray diffraction1.482012-09-05
62HYI|1|F5'-R(*UP*UP*UP*UP*UP*U)-3'Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-ray diffraction2.32006-08-15
73EX7|1|FRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')The crystal structure of EJC in its transition stateX-ray diffraction2.32008-12-09
83EX7|1|JRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')The crystal structure of EJC in its transition stateX-ray diffraction2.32008-12-09
92HYI|1|L5'-R(*UP*UP*UP*UP*UP*U)-3'Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-ray diffraction2.32006-08-15
104NL3|1|R5'-R(*UP*UP*UP*UP*UP*U)-3'Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-ray diffraction3.12014-09-10
114NL3|1|Z5'-R(*UP*UP*UP*UP*UP*U)-3'Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-ray diffraction3.12014-09-10
123O8R|1|CRNA (5'-R(P*UP*(5BU)P*UP*UP*UP*U)-3')Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-ray diffraction2.32011-01-05
133O8C|1|CRNA (5'-R(P*UP*(5BU)P*UP*UP*UP*U)-3')Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-ray diffraction22011-01-05
145BTE|1|CRNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')Homo sapiensEukaryaCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-ray diffraction2.42015-07-22
155BTE|1|DRNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')Homo sapiensEukaryaCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-ray diffraction2.42015-07-22
161N34|1|ZA-SITE MESSENGER RNA FRAGMENTThermus thermophilusBacteriaStructure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon positionX-ray diffraction3.82002-11-29
173PF5|1|Shexaribouracil (rU6)Crystal structure of Bs-CspB in complex with rU6X-ray diffraction1.682011-09-21

Release history

Release2.642.652.66
Date2016-02-262016-03-042016-03-11

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_all_74924.2NR_all_74924.12.64(16) 5BTE|1|D, 5BTE|1|C, 4NL3|1|Z, 4NL3|1|R, 4ALP|1|E, 3PF5|1|S, 3PF5|1|R, 3PEY|1|B, 3PEW|1|B, 3O8R|1|C, 3O8C|1|C, 3EX7|1|J, 3EX7|1|F, 2HYI|1|L, 2HYI|1|F, 1N34|1|Z(1) 5ELX|1|B(0)

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_all_74924.2NR_1.5_74924.32.67(3) 3PEW|1|B, 3PEY|1|B, 4ALP|1|E(14) 3PF5|1|R, 5BTE|1|C, 2HYI|1|F, 3O8C|1|C, 4NL3|1|R, 5ELX|1|B, 3EX7|1|F, 3O8R|1|C, 4NL3|1|Z, 1N34|1|Z, 3EX7|1|J, 3PF5|1|S, 5BTE|1|D, 2HYI|1|L(0)
NR_all_74924.2NR_2.0_74924.32.67(7) 3PF5|1|R, 3PF5|1|S, 4ALP|1|E, 5ELX|1|B, 3O8C|1|C, 3PEW|1|B, 3PEY|1|B(10) 3EX7|1|F, 4NL3|1|Z, 2HYI|1|F, 3O8R|1|C, 5BTE|1|D, 2HYI|1|L, 4NL3|1|R, 1N34|1|Z, 3EX7|1|J, 5BTE|1|C(0)
NR_all_74924.2NR_2.5_74924.32.67(14) 2HYI|1|L, 3EX7|1|F, 3EX7|1|J, 3O8R|1|C, 3PEW|1|B, 3PF5|1|S, 4ALP|1|E, 5BTE|1|C, 5ELX|1|B, 3PEY|1|B, 2HYI|1|F, 3O8C|1|C, 5BTE|1|D, 3PF5|1|R(3) 1N34|1|Z, 4NL3|1|R, 4NL3|1|Z(0)
NR_all_74924.2NR_20.0_74924.32.67(17) 1N34|1|Z, 2HYI|1|L, 3EX7|1|J, 3O8R|1|C, 3PEY|1|B, 3PF5|1|S, 4NL3|1|R, 5BTE|1|C, 5ELX|1|B, 2HYI|1|F, 3EX7|1|F, 3O8C|1|C, 3PEW|1|B, 3PF5|1|R, 4ALP|1|E, 4NL3|1|Z, 5BTE|1|D(0) (2) 4Y91|1|O, 4Y91|1|N
NR_all_74924.2NR_3.0_74924.32.67(14) 3EX7|1|J, 3O8C|1|C, 3O8R|1|C, 3PEW|1|B, 3PEY|1|B, 3PF5|1|R, 3PF5|1|S, 4ALP|1|E, 5BTE|1|C, 2HYI|1|F, 5BTE|1|D, 2HYI|1|L, 3EX7|1|F, 5ELX|1|B(3) 4NL3|1|Z, 1N34|1|Z, 4NL3|1|R(2) 4Y91|1|O, 4Y91|1|N
NR_all_74924.2NR_3.5_74924.32.67(16) 3EX7|1|J, 3O8R|1|C, 3PEY|1|B, 3PF5|1|S, 4NL3|1|R, 5BTE|1|C, 5ELX|1|B, 2HYI|1|L, 3EX7|1|F, 3O8C|1|C, 3PEW|1|B, 3PF5|1|R, 4ALP|1|E, 4NL3|1|Z, 5BTE|1|D, 2HYI|1|F(1) 1N34|1|Z(2) 4Y91|1|O, 4Y91|1|N
NR_all_74924.2NR_4.0_74924.32.67(17) 2HYI|1|F, 3EX7|1|F, 3O8C|1|C, 3PEW|1|B, 3PF5|1|R, 4ALP|1|E, 4NL3|1|Z, 5BTE|1|D, 1N34|1|Z, 2HYI|1|L, 3EX7|1|J, 3O8R|1|C, 3PEY|1|B, 3PF5|1|S, 4NL3|1|R, 5BTE|1|C, 5ELX|1|B(0) (2) 4Y91|1|O, 4Y91|1|N
NR_all_74924.2NR_all_74924.32.67(17) 3EX7|1|J, 3O8R|1|C, 3PEY|1|B, 3PF5|1|S, 4NL3|1|R, 5BTE|1|C, 5ELX|1|B, 1N34|1|Z, 2HYI|1|L, 3EX7|1|F, 3O8C|1|C, 3PEW|1|B, 3PF5|1|R, 4ALP|1|E, 4NL3|1|Z, 5BTE|1|D, 2HYI|1|F(0) (2) 4Y91|1|O, 4Y91|1|N

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
13O8R|1|CVisualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-RAY DIFFRACTION2.35
23O8C|1|CVisualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-RAY DIFFRACTION25
33PF5|1|SCrystal structure of Bs-CspB in complex with rU6X-RAY DIFFRACTION1.681
42HYI|1|FStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-RAY DIFFRACTION2.36
53EX7|1|JThe crystal structure of EJC in its transition stateX-RAY DIFFRACTION2.36
62HYI|1|LStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-RAY DIFFRACTION2.36
73EX7|1|FThe crystal structure of EJC in its transition stateX-RAY DIFFRACTION2.36
83PEW|1|BS. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3X-RAY DIFFRACTION1.56
93PEY|1|BS. cerevisiae Dbp5 bound to RNA and ADP BeF3X-RAY DIFFRACTION1.46
105ELX|1|BS. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3X-RAY DIFFRACTION1.816
111N34|1|ZStructure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon positionX-RAY DIFFRACTION3.84
125BTE|1|CCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-RAY DIFFRACTION2.44
135BTE|1|DCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-RAY DIFFRACTION2.44
143PF5|1|RCrystal structure of Bs-CspB in complex with rU6X-RAY DIFFRACTION1.689
154NL3|1|ZCrystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-RAY DIFFRACTION3.16
164NL3|1|RCrystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-RAY DIFFRACTION3.16
174ALP|1|EThe Lin28b Cold shock domain in complex with hexauridineX-RAY DIFFRACTION1.486
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