RNA 3D Hub //

Equivalence class NR_3.5_83835.1 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
15B2T|1|A+ 5B2T|1|C+ 5B2T|1|D (rep)Trans-activating crRNAGuide RNA, Non-target DNA, DNA (5'-D(*TP*GP*CP*GP*AP*TP*TP*G)-3'), Target DNAStreptococcus pyogenesBacteriaRF02348Crystal structure of the Streptococcus pyogenes Cas9 VRER variant in complex with sgRNA and target DNA (TGCG PAM)X-ray diffraction2.21172016-03-23
25B2R|1|A+ 5B2R|1|C+ 5B2R|1|DTrans-activating crRNAGuide RNA, Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3'), Target DNAStreptococcus pyogenesBacteriaRF02348Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA and target DNA (TGA PAM)X-ray diffraction21172016-03-23
35B2S|1|A+ 5B2S|1|C+ 5B2S|1|DTrans-activating crRNAGuide RNA, Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3'), Target DNAStreptococcus pyogenesBacteriaRF02348Crystal structure of the Streptococcus pyogenes Cas9 EQR variant in complex with sgRNA and target DNA (TGAG PAM)X-ray diffraction2.21172016-03-23
46AI6|1|B+ 6AI6|1|C+ 6AI6|1|DTrans-activating crRNADNA (28-MER), DNA (8-MER), RNA (81-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of SpCas9-NGX-ray diffraction2.71172018-10-31
54OO8|1|B+ 4OO8|1|CDNA (5'-D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP*C)-3'), RNA (97-MER)RF02348Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-ray diffraction2.51182014-02-26
64OO8|1|E+ 4OO8|1|FDNA (5'-D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP*C)-3'), RNA (97-MER)RF02348Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-ray diffraction2.51202014-02-26
75XBL|1|BTrans-activating crRNARNA (98-MER)Streptococcus pyogenesBacteriaRF02348Structure of nuclease in complex with associated proteinX-ray diffraction3.05882017-06-14
86IFO|1|CTrans-activating crRNARNA (99-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of AcrIIA2-SpyCas9-sgRNA ternary complexX-ray diffraction3.31882019-01-23
96IFO|1|DTrans-activating crRNARNA (99-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of AcrIIA2-SpyCas9-sgRNA ternary complexX-ray diffraction3.31902019-01-23
108SRS|1|B+ 8SRS|1|D+ 8SRS|1|c+ 8SRS|1|CTrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TAC PAM DNAElectron microscopy2.791492024-05-01
118T7S|1|B+ 8T7S|1|C+ 8T7S|1|D+ 8T7S|1|cTrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRYmer bound to NAC PAM DNAElectron microscopy3.011512024-05-01
128SPQ|1|B+ 8SPQ|1|C+ 8SPQ|1|D+ 8SPQ|1|ETrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TGG PAM DNAElectron microscopy3.261492024-05-01
138T6X|1|B+ 8T6X|1|C+ 8T6X|1|DTrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 18 bp R-loopElectron microscopy3.081392024-05-01
148T6T|1|B+ 8T6T|1|C+ 8T6T|1|DTrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 13 bp R-loopElectron microscopy3.041292024-05-01
158T79|1|B+ 8T79|1|C+ 8T79|1|DTrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex bound to non-target DNA with 10 bp R-loopElectron microscopy3.041182024-05-08
168T78|1|B+ 8T78|1|C+ 8T78|1|DTrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex bound to non-target DNA with 8 bp R-loopElectron microscopy3.021162024-05-01
178T6S|1|B+ 8T6S|1|C+ 8T6S|1|DTrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 10 bp R-loopElectron microscopy3.281192024-05-01
188T77|1|B+ 8T77|1|C+ 8T77|1|DTrans-activating crRNAgRNA, NTS, TSStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex bound to non-target DNA with 6 bp R-loopElectron microscopy3.251142024-05-01
198T6Y|1|BTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex bound to non-target DNA with 1 bp R-loopElectron microscopy2.88882024-05-01
208T7S|1|HTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRYmer bound to NAC PAM DNAElectron microscopy3.01882024-05-01
218T6P|1|BTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 2 bp R-loopElectron microscopy3.15882024-05-01
228T76|1|BTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 3 bp R-loopElectron microscopy3.42882024-05-01

Release history

Release3.3783.3793.380
Date2025-03-132025-03-192025-03-26

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

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.

#SViewPDBTitleMethodResolution#NTs
18T7S|1|HSpRYmer bound to NAC PAM DNAELECTRON MICROSCOPY3.0188
28T7S|1|B+ 8T7S|1|C+ 8T7S|1|D+ 8T7S|1|cSpRYmer bound to NAC PAM DNAELECTRON MICROSCOPY3.01151
38T6X|1|B+ 8T6X|1|C+ 8T6X|1|DSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 18 bp R-loopELECTRON MICROSCOPY3.08139
48SRS|1|B+ 8SRS|1|D+ 8SRS|1|c+ 8SRS|1|CSpRY-Cas9:gRNA complex targeting TAC PAM DNAELECTRON MICROSCOPY2.79149
58SPQ|1|B+ 8SPQ|1|C+ 8SPQ|1|D+ 8SPQ|1|ESpRY-Cas9:gRNA complex targeting TGG PAM DNAELECTRON MICROSCOPY3.26149
68T6T|1|B+ 8T6T|1|C+ 8T6T|1|DSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 13 bp R-loopELECTRON MICROSCOPY3.04129
78T6P|1|BSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 2 bp R-loopELECTRON MICROSCOPY3.1588
88T76|1|BSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 3 bp R-loopELECTRON MICROSCOPY3.4288
98T6S|1|B+ 8T6S|1|C+ 8T6S|1|DSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 10 bp R-loopELECTRON MICROSCOPY3.28119
108T78|1|B+ 8T78|1|C+ 8T78|1|DSpRY-Cas9:gRNA complex bound to non-target DNA with 8 bp R-loopELECTRON MICROSCOPY3.02116
118T79|1|B+ 8T79|1|C+ 8T79|1|DSpRY-Cas9:gRNA complex bound to non-target DNA with 10 bp R-loopELECTRON MICROSCOPY3.04118
128T6Y|1|BSpRY-Cas9:gRNA complex bound to non-target DNA with 1 bp R-loopELECTRON MICROSCOPY2.8888
138T77|1|B+ 8T77|1|C+ 8T77|1|DSpRY-Cas9:gRNA complex bound to non-target DNA with 6 bp R-loopELECTRON MICROSCOPY3.25114
145XBL|1|BStructure of nuclease in complex with associated proteinX-RAY DIFFRACTION3.0588
156IFO|1|DCrystal structure of AcrIIA2-SpyCas9-sgRNA ternary complexX-RAY DIFFRACTION3.3190
166IFO|1|CCrystal structure of AcrIIA2-SpyCas9-sgRNA ternary complexX-RAY DIFFRACTION3.3188
175B2S|1|A+ 5B2S|1|C+ 5B2S|1|DCrystal structure of the Streptococcus pyogenes Cas9 EQR variant in complex with sgRNA and target DNA (TGAG PAM)X-RAY DIFFRACTION2.2117
185B2R|1|A+ 5B2R|1|C+ 5B2R|1|DCrystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA and target DNA (TGA PAM)X-RAY DIFFRACTION2117
195B2T|1|A+ 5B2T|1|C+ 5B2T|1|DCrystal structure of the Streptococcus pyogenes Cas9 VRER variant in complex with sgRNA and target DNA (TGCG PAM)X-RAY DIFFRACTION2.2117
206AI6|1|B+ 6AI6|1|C+ 6AI6|1|DCrystal structure of SpCas9-NGX-RAY DIFFRACTION2.7117
214OO8|1|B+ 4OO8|1|CCrystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-RAY DIFFRACTION2.5118
224OO8|1|E+ 4OO8|1|FCrystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-RAY DIFFRACTION2.5120

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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