RNA 3D Hub //

Equivalence class NR_3.5_56990.2 Current

#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)Crystal 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)Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-ray diffraction2.51202014-02-26
77Z4D|1|A+ 7Z4D|1|C+ 7Z4D|1|DTrans-activating crRNANon-target strand of 10 nucleotide complementary DNA substrate, sgRNA, Target strand of 10 nucleotide complementary DNA substratesynthetic constructSyntheticRF02348Crystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrateX-ray diffraction3.11272022-08-31
87Z4D|1|F+ 7Z4D|1|G+ 7Z4D|1|HTrans-activating crRNANon-target strand of 10 nucleotide complementary DNA substrate, sgRNA, Target strand of 10 nucleotide complementary DNA substratesynthetic constructSyntheticRF02348Crystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrateX-ray diffraction3.11232022-08-31
94ZT0|1|DTrans-activating crRNAsingle-guide RNAStreptococcus pyogenesBacteriaRF02348Crystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolutionX-ray diffraction2.9722015-07-08
104ZT0|1|BTrans-activating crRNAsingle-guide RNAStreptococcus pyogenesBacteriaRF02348Crystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolutionX-ray diffraction2.9722015-07-08
114ZT9|1|DTrans-activating crRNAsingle-guide RNAStreptococcus pyogenesBacteriaRF02348Nuclease-inactive Streptococcus pyogenes Cas9 (D10A/H840A, dCas9) in complex with single-guide RNA at 3.1 Angstrom resolutionX-ray diffraction3.1722015-07-08
125XBL|1|BTrans-activating crRNARNA (98-MER)Streptococcus pyogenesBacteriaRF02348Structure of nuclease in complex with associated proteinX-ray diffraction3.05882017-06-14
134ZT9|1|BTrans-activating crRNAsingle-guide RNAStreptococcus pyogenesBacteriaRF02348Nuclease-inactive Streptococcus pyogenes Cas9 (D10A/H840A, dCas9) in complex with single-guide RNA at 3.1 Angstrom resolutionX-ray diffraction3.1722015-07-08
146IFO|1|CTrans-activating crRNARNA (99-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of AcrIIA2-SpyCas9-sgRNA ternary complexX-ray diffraction3.31882019-01-23
156IFO|1|DTrans-activating crRNARNA (99-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of AcrIIA2-SpyCas9-sgRNA ternary complexX-ray diffraction3.31902019-01-23
167S4X|1|B+ 7S4X|1|D+ 7S4X|1|c+ 7S4X|1|CTrans-activating crRNAgRNA, NTS, TSsynthetic constructSyntheticRF02348Cas9:gRNA in complex with 18-20MM DNA, 1 minute time-point, kinked active conformationElectron microscopy2.761612022-03-02
178SRS|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
189EAK|1|B+ 9EAK|1|C+ 9EAK|1|DTrans-activating crRNADNA (Non-target strand), DNA (Target Strand), sgRNAsynthetic constructSyntheticRF02348SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State I - pre-activation)Electron microscopy2.761492025-06-18
197Z4L|1|A+ 7Z4L|1|C+ 7Z4L|1|DTrans-activating crRNANon-target strand of 18-nucleotide complementary DNA substrate, sgRNA, Target strand of 18-nucleotide complementary DNA substratesynthetic constructSyntheticRF02348SpCas9 bound to 18-nucleotide complementary DNA substrate in the checkpoint stateElectron microscopy2.541362022-08-31
208T7S|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
219ED9|1|B+ 9ED9|1|D+ 9ED9|1|C+ 9ED9|1|cTrans-activating crRNANon-target strand, PAM-distal Target Strand, PAM-proximal Target Strand, sgRNAsynthetic constructSyntheticRF02348SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State III - checkpoint)Electron microscopy2.951432025-06-18
229EDA|1|B+ 9EDA|1|D+ 9EDA|1|c+ 9EDA|1|CTrans-activating crRNANon-target strand, PAM-distal Target Strand, PAM-proximal Target Strand, sgRNAsynthetic constructSyntheticRF02348SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State IV - product)Electron microscopy2.881382025-06-18
239CGU|1|B+ 9CGU|1|C+ 9CGU|1|DTrans-activating crRNANon-target strand, sgRNA, Target strandsynthetic constructSyntheticRF02348Cas9 ternary complex, 14-nt sgRNA, State II (kinked)Electron microscopy31442024-12-04
247Z4J|1|A+ 7Z4J|1|D+ 7Z4J|1|C+ 7Z4J|1|cTrans-activating crRNANon-target strand of 18-nucleotide complementary DNA substrate, sgRNA, Target strand of 18-nucleotide complementary DNA substrate, PAM-distal end, Target strand of 18-nucleotide complementary DNA substrate, PAM-proximal endsynthetic constructSyntheticRF02348SpCas9 bound to 18-nucleotide complementary DNA substrate in the catalytic stateElectron microscopy2.991422022-08-31
256O0X|1|B+ 6O0X|1|D+ 6O0X|1|c+ 6O0X|1|CTrans-activating crRNA3' product of target strand DNA, 5' product of target strand DNA, non-target strand DNA, single guide RNAsynthetic constructSyntheticRF02348Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesiumElectron microscopy3.281502019-07-10
268SPQ|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
278U3Y|1|B+ 8U3Y|1|c+ 8U3Y|1|C+ 8U3Y|1|DTrans-activating crRNADNA (5'-D(P*CP*GP*TP*TP*TP*GP*TP*AP*CP*TP*CP*CP*AP*GP*CP*G)-3'), DNA (5'-D(P*TP*CP*TP*CP*AP*TP*CP*TP*TP*TP*AP*TP*GP*CP*GP*TP*C)-3'), DNA (5'-D(P*TP*GP*GP*AP*GP*TP*AP*CP*AP*AP*AP*CP*G)-3'), RNA (98-MER)synthetic constructSyntheticRF02348SpG Cas9 with NGG PAM DNA targetElectron microscopy3.11442024-05-01
286O0Y|1|B+ 6O0Y|1|D+ 6O0Y|1|c+ 6O0Y|1|CTrans-activating crRNA3' product of target strand DNA, 5' product of target strand DNA, non-target strand DNA, single guide RNAsynthetic constructSyntheticRF02348Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesiumElectron microscopy3.371502019-07-10
298T6X|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
309C9P|1|B+ 9C9P|1|C+ 9C9P|1|DTrans-activating crRNANon-target strand, sgRNA, Target strandsynthetic constructSyntheticRF02348Cas9 ternary complex, 14-nt sgRNA, State I (linear)Electron microscopy3.11392024-12-04
317Z4I|1|A+ 7Z4I|1|D+ 7Z4I|1|CTrans-activating crRNANon-target strand of 16-nucleotide complementary DNA substrate, sgRNA, Target strand of 16-nucleotide complementary DNA substratesynthetic constructSyntheticRF02348SpCas9 bound to 16-nucleotide complementary DNA substrateElectron microscopy3.121372022-08-31
328T6T|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
336O0Z|1|B+ 6O0Z|1|C+ 6O0Z|1|DTrans-activating crRNAnon-target strand DNA, single guide RNA, target strand DNAsynthetic constructSyntheticRF02348Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesiumElectron microscopy3.31352019-07-10
347S4V|1|B+ 7S4V|1|CTrans-activating crRNAgRNA, TSsynthetic constructSyntheticRF02348Cas9 bound to 12-14MM DNA, 60 min time-point, kinked conformationElectron microscopy3.281312022-03-02
359EDB|1|B+ 9EDB|1|C+ 9EDB|1|DTrans-activating crRNANon-target Strand, sgRNA, Target Strandsynthetic constructSyntheticRF02348SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State V - dissociated)Electron microscopy3.11222025-06-18
367Z4H|1|A+ 7Z4H|1|C+ 7Z4H|1|DTrans-activating crRNANon-target strand of 14-nucleotide complementary DNA substrate, sgRNA, Target strand of 14-nucleotide complementary DNA substratesynthetic constructSyntheticRF02348SpCas9 bound to 14-nucleotide complementary DNA substrateElectron microscopy3.491422022-08-31
378T79|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
388T78|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
398T6S|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
408T77|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
418YE6|1|CTrans-activating crRNARNA (92-MER)Streptococcus pyogenesBacteriaRF02348Cryo-EM structure of Cas9-sgRNA-A32 complexElectron microscopy2.95922024-09-11
428T6Y|1|BTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex bound to non-target DNA with 1 bp R-loopElectron microscopy2.88882024-05-01
438T7S|1|HTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRYmer bound to NAC PAM DNAElectron microscopy3.01882024-05-01
448T6P|1|BTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 2 bp R-loopElectron microscopy3.15882024-05-01
458T76|1|BTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 3 bp R-loopElectron microscopy3.42882024-05-01

Release history

Release3.392
Date2025-06-18

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

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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
18YE6|1|CCryo-EM structure of Cas9-sgRNA-A32 complexELECTRON MICROSCOPY2.9592
28T6Y|1|BSpRY-Cas9:gRNA complex bound to non-target DNA with 1 bp R-loopELECTRON MICROSCOPY2.8888
38T77|1|B+ 8T77|1|C+ 8T77|1|DSpRY-Cas9:gRNA complex bound to non-target DNA with 6 bp R-loopELECTRON MICROSCOPY3.25114
48T79|1|B+ 8T79|1|C+ 8T79|1|DSpRY-Cas9:gRNA complex bound to non-target DNA with 10 bp R-loopELECTRON MICROSCOPY3.04118
58T78|1|B+ 8T78|1|C+ 8T78|1|DSpRY-Cas9:gRNA complex bound to non-target DNA with 8 bp R-loopELECTRON MICROSCOPY3.02116
69CGU|1|B+ 9CGU|1|C+ 9CGU|1|DCas9 ternary complex, 14-nt sgRNA, State II (kinked)ELECTRON MICROSCOPY3144
77S4V|1|B+ 7S4V|1|CCas9 bound to 12-14MM DNA, 60 min time-point, kinked conformationELECTRON MICROSCOPY3.28131
86O0X|1|B+ 6O0X|1|D+ 6O0X|1|c+ 6O0X|1|CConformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesiumELECTRON MICROSCOPY3.28150
96O0Y|1|B+ 6O0Y|1|D+ 6O0Y|1|c+ 6O0Y|1|CConformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesiumELECTRON MICROSCOPY3.37150
109C9P|1|B+ 9C9P|1|C+ 9C9P|1|DCas9 ternary complex, 14-nt sgRNA, State I (linear)ELECTRON MICROSCOPY3.1139
116O0Z|1|B+ 6O0Z|1|C+ 6O0Z|1|DConformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesiumELECTRON MICROSCOPY3.3135
129EDB|1|B+ 9EDB|1|C+ 9EDB|1|DSpCas9 with 17-bp R-loop containing 2 terminal mismatches (State V - dissociated)ELECTRON MICROSCOPY3.1122
139EAK|1|B+ 9EAK|1|C+ 9EAK|1|DSpCas9 with 17-bp R-loop containing 2 terminal mismatches (State I - pre-activation)ELECTRON MICROSCOPY2.76149
149EDA|1|B+ 9EDA|1|D+ 9EDA|1|c+ 9EDA|1|CSpCas9 with 17-bp R-loop containing 2 terminal mismatches (State IV - product)ELECTRON MICROSCOPY2.88138
159ED9|1|B+ 9ED9|1|D+ 9ED9|1|C+ 9ED9|1|cSpCas9 with 17-bp R-loop containing 2 terminal mismatches (State III - checkpoint)ELECTRON MICROSCOPY2.95143
167Z4H|1|A+ 7Z4H|1|C+ 7Z4H|1|DSpCas9 bound to 14-nucleotide complementary DNA substrateELECTRON MICROSCOPY3.49142
177Z4L|1|A+ 7Z4L|1|C+ 7Z4L|1|DSpCas9 bound to 18-nucleotide complementary DNA substrate in the checkpoint stateELECTRON MICROSCOPY2.54136
187Z4I|1|A+ 7Z4I|1|D+ 7Z4I|1|CSpCas9 bound to 16-nucleotide complementary DNA substrateELECTRON MICROSCOPY3.12137
198T6S|1|B+ 8T6S|1|C+ 8T6S|1|DSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 10 bp R-loopELECTRON MICROSCOPY3.28119
208T76|1|BSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 3 bp R-loopELECTRON MICROSCOPY3.4288
218T6P|1|BSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 2 bp R-loopELECTRON MICROSCOPY3.1588
228T6T|1|B+ 8T6T|1|C+ 8T6T|1|DSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 13 bp R-loopELECTRON MICROSCOPY3.04129
238T6X|1|B+ 8T6X|1|C+ 8T6X|1|DSpRY-Cas9:gRNA complex targeting TAC PAM DNA with 18 bp R-loopELECTRON MICROSCOPY3.08139
248SPQ|1|B+ 8SPQ|1|C+ 8SPQ|1|D+ 8SPQ|1|ESpRY-Cas9:gRNA complex targeting TGG PAM DNAELECTRON MICROSCOPY3.26149
258SRS|1|B+ 8SRS|1|D+ 8SRS|1|c+ 8SRS|1|CSpRY-Cas9:gRNA complex targeting TAC PAM DNAELECTRON MICROSCOPY2.79149
268U3Y|1|B+ 8U3Y|1|c+ 8U3Y|1|C+ 8U3Y|1|DSpG Cas9 with NGG PAM DNA targetELECTRON MICROSCOPY3.1144
277Z4J|1|A+ 7Z4J|1|D+ 7Z4J|1|C+ 7Z4J|1|cSpCas9 bound to 18-nucleotide complementary DNA substrate in the catalytic stateELECTRON MICROSCOPY2.99142
287S4X|1|B+ 7S4X|1|D+ 7S4X|1|c+ 7S4X|1|CCas9:gRNA in complex with 18-20MM DNA, 1 minute time-point, kinked active conformationELECTRON MICROSCOPY2.76161
298T7S|1|B+ 8T7S|1|C+ 8T7S|1|D+ 8T7S|1|cSpRYmer bound to NAC PAM DNAELECTRON MICROSCOPY3.01151
308T7S|1|HSpRYmer bound to NAC PAM DNAELECTRON MICROSCOPY3.0188
317Z4D|1|A+ 7Z4D|1|C+ 7Z4D|1|DCrystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrateX-RAY DIFFRACTION3.1127
327Z4D|1|F+ 7Z4D|1|G+ 7Z4D|1|HCrystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrateX-RAY DIFFRACTION3.1123
334ZT9|1|BNuclease-inactive Streptococcus pyogenes Cas9 (D10A/H840A, dCas9) in complex with single-guide RNA at 3.1 Angstrom resolutionX-RAY DIFFRACTION3.172
344ZT0|1|BCrystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolutionX-RAY DIFFRACTION2.972
354ZT0|1|DCrystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolutionX-RAY DIFFRACTION2.972
364ZT9|1|DNuclease-inactive Streptococcus pyogenes Cas9 (D10A/H840A, dCas9) in complex with single-guide RNA at 3.1 Angstrom resolutionX-RAY DIFFRACTION3.172
374OO8|1|B+ 4OO8|1|CCrystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-RAY DIFFRACTION2.5118
386AI6|1|B+ 6AI6|1|C+ 6AI6|1|DCrystal structure of SpCas9-NGX-RAY DIFFRACTION2.7117
395B2T|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
405B2S|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
415B2R|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
424OO8|1|E+ 4OO8|1|FCrystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-RAY DIFFRACTION2.5120
436IFO|1|CCrystal structure of AcrIIA2-SpyCas9-sgRNA ternary complexX-RAY DIFFRACTION3.3188
446IFO|1|DCrystal structure of AcrIIA2-SpyCas9-sgRNA ternary complexX-RAY DIFFRACTION3.3190
455XBL|1|BStructure of nuclease in complex with associated proteinX-RAY DIFFRACTION3.0588

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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