RNA 3D Hub //

Equivalence class NR_all_53414.1 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
17Z4D|1|A+ 7Z4D|1|C+ 7Z4D|1|D (rep)Trans-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
27Z4D|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
37S4X|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
47Z4L|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
59CGU|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
67Z4J|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
76O0X|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
88U3Y|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
96O0Y|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
109C9P|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
117Z4I|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
126O0Z|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
138TZZ|1|B+ 8TZZ|1|c+ 8TZZ|1|C+ 8TZZ|1|DTrans-activating crRNADNA (5'-D(P*CP*GP*TP*TP*TP*GP*TP*AP*CP*TP*GP*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*CP*AP*GP*TP*AP*CP*AP*AP*AP*CP*G)-3'), RNA (98-MER)synthetic constructSyntheticRF02348SpG Cas9 with NGC PAM DNA targetElectron microscopy3.561442024-05-01
147S4V|1|B+ 7S4V|1|CTrans-activating crRNAgRNA, TSsynthetic constructSyntheticRF02348Cas9 bound to 12-14MM DNA, 60 min time-point, kinked conformationElectron microscopy3.281312022-03-02
157Z4H|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
167Z4G|1|A+ 7Z4G|1|C+ 7Z4G|1|DTrans-activating crRNANon-target strand of 12-nucleotide complementary DNA substrate, sgRNA, Target strand of 12-nucleotide complementary DNA substratesynthetic constructSyntheticRF02348SpCas9 bound to 12-nucleotide complementary DNA substrateElectron microscopy3.641442022-08-31
177Z4C|1|A+ 7Z4C|1|C+ 7Z4C|1|DTrans-activating crRNANon-target strand of 6 nucleotide complementary DNA substrate, sgRNA, Target strand of 6 nucleotide complementary DNA substratesynthetic constructSyntheticRF02348SpCas9 bound to 6 nucleotide complementary DNA substrateElectron microscopy3.871482022-08-31
187S4U|1|B+ 7S4U|1|C+ 7S4U|1|DTrans-activating crRNAgRNA, Non-target strand, Target strandsynthetic constructSyntheticRF02348Cryo-EM structure of Cas9 in complex with 12-14MM DNA substrate, 5 minute time-pointElectron microscopy3.561422022-03-02
197Z4K|1|A+ 7Z4K|1|C+ 7Z4K|1|DTrans-activating crRNANon-target strand of 10-nucleotide complementary DNA substrate, sgRNA, Target strand of 10-nucleotide complementary DNA substratesynthetic constructSyntheticRF02348SpCas9 bound to 10-nucleotide complementary DNA substrateElectron microscopy3.811382022-08-31
207Z4E|1|A+ 7Z4E|1|C+ 7Z4E|1|DTrans-activating crRNANon-target strand of 8 nucleotide complementary DNA substrate, sgRNA, Target strand of 8 nucleotide complementary DNA substratesynthetic constructSyntheticRF02348SpCas9 bound to 6 nucleotide complementary DNA substrateElectron microscopy4.141422022-08-31

Release history

Release3.3783.3793.3803.381
Date2025-03-132025-03-192025-03-262025-04-02

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
17Z4D|1|F+ 7Z4D|1|G+ 7Z4D|1|HCrystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrateX-RAY DIFFRACTION3.1123
27Z4D|1|A+ 7Z4D|1|C+ 7Z4D|1|DCrystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrateX-RAY DIFFRACTION3.1127
37Z4L|1|A+ 7Z4L|1|C+ 7Z4L|1|DSpCas9 bound to 18-nucleotide complementary DNA substrate in the checkpoint stateELECTRON MICROSCOPY2.54136
47Z4I|1|A+ 7Z4I|1|D+ 7Z4I|1|CSpCas9 bound to 16-nucleotide complementary DNA substrateELECTRON MICROSCOPY3.12137
57Z4G|1|A+ 7Z4G|1|C+ 7Z4G|1|DSpCas9 bound to 12-nucleotide complementary DNA substrateELECTRON MICROSCOPY3.64144
67Z4H|1|A+ 7Z4H|1|C+ 7Z4H|1|DSpCas9 bound to 14-nucleotide complementary DNA substrateELECTRON MICROSCOPY3.49142
77Z4K|1|A+ 7Z4K|1|C+ 7Z4K|1|DSpCas9 bound to 10-nucleotide complementary DNA substrateELECTRON MICROSCOPY3.81138
87Z4C|1|A+ 7Z4C|1|C+ 7Z4C|1|DSpCas9 bound to 6 nucleotide complementary DNA substrateELECTRON MICROSCOPY3.87148
97Z4E|1|A+ 7Z4E|1|C+ 7Z4E|1|DSpCas9 bound to 6 nucleotide complementary DNA substrateELECTRON MICROSCOPY4.14142
107S4X|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
117Z4J|1|A+ 7Z4J|1|D+ 7Z4J|1|C+ 7Z4J|1|cSpCas9 bound to 18-nucleotide complementary DNA substrate in the catalytic stateELECTRON MICROSCOPY2.99142
128U3Y|1|B+ 8U3Y|1|c+ 8U3Y|1|C+ 8U3Y|1|DSpG Cas9 with NGG PAM DNA targetELECTRON MICROSCOPY3.1144
138TZZ|1|B+ 8TZZ|1|c+ 8TZZ|1|C+ 8TZZ|1|DSpG Cas9 with NGC PAM DNA targetELECTRON MICROSCOPY3.56144
146O0Y|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
156O0X|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
166O0Z|1|B+ 6O0Z|1|C+ 6O0Z|1|DConformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesiumELECTRON MICROSCOPY3.3135
179C9P|1|B+ 9C9P|1|C+ 9C9P|1|DCas9 ternary complex, 14-nt sgRNA, State I (linear)ELECTRON MICROSCOPY3.1139
187S4V|1|B+ 7S4V|1|CCas9 bound to 12-14MM DNA, 60 min time-point, kinked conformationELECTRON MICROSCOPY3.28131
199CGU|1|B+ 9CGU|1|C+ 9CGU|1|DCas9 ternary complex, 14-nt sgRNA, State II (kinked)ELECTRON MICROSCOPY3144
207S4U|1|B+ 7S4U|1|C+ 7S4U|1|DCryo-EM structure of Cas9 in complex with 12-14MM DNA substrate, 5 minute time-pointELECTRON MICROSCOPY3.56142

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.


Coloring options:

Copyright 2025 BGSU RNA group. Page generated in 0.1158 s