RNA 3D Hub //

Equivalence class NR_all_66773.1 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
15FQ5|1|A+ 5FQ5|1|E (rep)Trans-activating crRNASGRNA, TARGET DNA STRAND DISTAL FRAGMENTsynthetic constructSyntheticRF02348Crystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasingX-ray diffraction2.141002016-03-23
25FW2|1|A+ 5FW2|1|C+ 5FW2|1|DTrans-activating crRNANON-TARGET DNA STRAND, SGRNA, TARGET DNA STRANDsynthetic constructSyntheticRF02348Crystal structure of SpCas9 variant EQR bound to sgRNA and TGAG PAM target DNAX-ray diffraction2.681202016-06-15
34UN3|1|A+ 4UN3|1|C+ 4UN3|1|DTrans-activating crRNANON-TARGET DNA STRAND, SGRNA, TARGET DNA STRANDsynthetic constructSyntheticRF02348Crystal structure of Cas9 bound to PAM-containing DNA targetX-ray diffraction2.591202014-07-23
45FW3|1|A+ 5FW3|1|C+ 5FW3|1|DTrans-activating crRNANON-TARGET DNA STRAND, SGRNA, TARGET DNA STRANDsynthetic constructSyntheticRF02348Crystal structure of SpCas9 variant VRER bound to sgRNA and TGCG PAM target DNAX-ray diffraction2.71202016-06-15
56K4Q|1|A+ 6K4Q|1|C+ 6K4Q|1|DTrans-activating crRNADNA (28-MER), DNA (5'-D(*AP*AP*AP*CP*GP*GP*TP*AP*TP*TP*G)-3'), sgRNAStreptococcus pyogenesBacteriaRF02348Crystal structure of xCas9 in complex with sgRNA and DNA (CGG PAM)X-ray diffraction2.71202019-09-25
66AEG|1|A+ 6AEG|1|C+ 6AEG|1|DTrans-activating crRNADNA (25-MER), DNA (5'-D(*AP*AP*AP*GP*AP*TP*TP*AP*TP*TP*G)-3'), RNA (95-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of xCas9 in complex with sgRNA and target DNA (GAT PAM)X-ray diffraction2.71312019-03-27
76K4P|1|A+ 6K4P|1|C+ 6K4P|1|DTrans-activating crRNADNA (28-MER), non-targeted DNA, sgRNAStreptococcus pyogenesBacteriaRF02348Crystal structure of xCas9 in complex with sgRNA and DNA (TGG PAM)X-ray diffraction2.91212019-09-25
85FW1|1|A+ 5FW1|1|C+ 5FW1|1|DTrans-activating crRNANON-TARGET DNA STRAND, SGRNA, TARGET DNA STRANDsynthetic constructSyntheticRF02348Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNAX-ray diffraction2.51202016-04-20
94UN4|1|A+ 4UN4|1|ETrans-activating crRNASGRNA, TARGET DNA STRAND DISTAL FRAGMENTsynthetic constructSyntheticRF02348Crystal structure of Cas9 bound to PAM-containing DNA target with mismatches at positions 1-2X-ray diffraction2.37992014-07-23
104UN5|1|A+ 4UN5|1|ETrans-activating crRNASGRNA, TARGET DNA STRAND DISTAL FRAGMENTsynthetic constructSyntheticRF02348Crystal structure of Cas9 bound to PAM-containing DNA target containing mismatches at positions 1-3X-ray diffraction2.4992014-07-23
116K57|1|A+ 6K57|1|C+ 6K57|1|DTrans-activating crRNAnon-target DNA, sgRNA, target DNAStreptococcus pyogenesBacteriaRF02348Crystal structure of dCas9 in complex with sgRNA and DNA (CGA PAM)X-ray diffraction2.981202019-09-25
126AEB|1|E+ 6AEB|1|G+ 6AEB|1|HTrans-activating crRNADNA (25-MER), DNA (5'-D(*AP*AP*AP*AP*AP*GP*TP*AP*TP*TP*G)-3'), RNA (95-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of xCas9 in complex with sgRNA and target DNA (AAG PAM)X-ray diffraction31312019-03-27
136AEB|1|A+ 6AEB|1|C+ 6AEB|1|DTrans-activating crRNADNA (25-MER), DNA (5'-D(*AP*AP*AP*AP*AP*GP*TP*AP*TP*TP*G)-3'), RNA (95-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of xCas9 in complex with sgRNA and target DNA (AAG PAM)X-ray diffraction31312019-03-27
146K4S|1|A+ 6K4S|1|C+ 6K4S|1|DTrans-activating crRNAnon-targeted DNA, sgRNA, targeted DNAStreptococcus pyogenesBacteriaRF02348Crystal structure of xCas9 in complex with sgRNA and DNA (TGC PAM)X-ray diffraction3.011182019-09-25
156K4U|1|A+ 6K4U|1|C+ 6K4U|1|DTrans-activating crRNAnon-target DNA, sgRNA, target DNAStreptococcus pyogenesBacteriaRF02348Crystal structure of xCas9 in complex with sgRNA and DNA (TGA PAM)X-ray diffraction3.21182019-09-25
166K3Z|1|A+ 6K3Z|1|C+ 6K3Z|1|DTrans-activating crRNADNA (28-MER), DNA (5'-D(*AP*AP*AP*TP*GP*AP*TP*AP*TP*TP*G)-3'), RNA (81-MER)Streptococcus pyogenesBacteriaRF02348Crystal structure of dCas9 in complex with sgRNA and DNA (TGA PAM)X-ray diffraction3.21202019-09-25

Release history

Release3.3823.3833.3843.3853.3863.3873.3883.3893.390
Date2025-04-092025-04-162025-04-232025-04-302025-05-072025-05-142025-05-212025-05-282025-06-04

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
16K4U|1|A+ 6K4U|1|C+ 6K4U|1|DCrystal structure of xCas9 in complex with sgRNA and DNA (TGA PAM)X-RAY DIFFRACTION3.2118
26K4S|1|A+ 6K4S|1|C+ 6K4S|1|DCrystal structure of xCas9 in complex with sgRNA and DNA (TGC PAM)X-RAY DIFFRACTION3.01118
36K4P|1|A+ 6K4P|1|C+ 6K4P|1|DCrystal structure of xCas9 in complex with sgRNA and DNA (TGG PAM)X-RAY DIFFRACTION2.9121
46K4Q|1|A+ 6K4Q|1|C+ 6K4Q|1|DCrystal structure of xCas9 in complex with sgRNA and DNA (CGG PAM)X-RAY DIFFRACTION2.7120
56K57|1|A+ 6K57|1|C+ 6K57|1|DCrystal structure of dCas9 in complex with sgRNA and DNA (CGA PAM)X-RAY DIFFRACTION2.98120
66K3Z|1|A+ 6K3Z|1|C+ 6K3Z|1|DCrystal structure of dCas9 in complex with sgRNA and DNA (TGA PAM)X-RAY DIFFRACTION3.2120
74UN3|1|A+ 4UN3|1|C+ 4UN3|1|DCrystal structure of Cas9 bound to PAM-containing DNA targetX-RAY DIFFRACTION2.59120
85FW2|1|A+ 5FW2|1|C+ 5FW2|1|DCrystal structure of SpCas9 variant EQR bound to sgRNA and TGAG PAM target DNAX-RAY DIFFRACTION2.68120
95FW3|1|A+ 5FW3|1|C+ 5FW3|1|DCrystal structure of SpCas9 variant VRER bound to sgRNA and TGCG PAM target DNAX-RAY DIFFRACTION2.7120
105FW1|1|A+ 5FW1|1|C+ 5FW1|1|DCrystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNAX-RAY DIFFRACTION2.5120
116AEG|1|A+ 6AEG|1|C+ 6AEG|1|DCrystal structure of xCas9 in complex with sgRNA and target DNA (GAT PAM)X-RAY DIFFRACTION2.7131
126AEB|1|A+ 6AEB|1|C+ 6AEB|1|DCrystal structure of xCas9 in complex with sgRNA and target DNA (AAG PAM)X-RAY DIFFRACTION3131
136AEB|1|E+ 6AEB|1|G+ 6AEB|1|HCrystal structure of xCas9 in complex with sgRNA and target DNA (AAG PAM)X-RAY DIFFRACTION3131
144UN4|1|A+ 4UN4|1|ECrystal structure of Cas9 bound to PAM-containing DNA target with mismatches at positions 1-2X-RAY DIFFRACTION2.3799
155FQ5|1|A+ 5FQ5|1|ECrystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasingX-RAY DIFFRACTION2.14100
164UN5|1|A+ 4UN5|1|ECrystal structure of Cas9 bound to PAM-containing DNA target containing mismatches at positions 1-3X-RAY DIFFRACTION2.499

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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