RNA 3D Hub //

Equivalence class NR_4.0_40726.1 Obsolete

Showing 1 to 7 of 7 entries
#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
55FW1|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
64UN4|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
74UN5|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

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.

Showing 1 to 7 of 7 entries
#SViewPDBTitleMethodResolution#NTs
14UN3|1|A+ 4UN3|1|C+ 4UN3|1|DCrystal structure of Cas9 bound to PAM-containing DNA targetX-RAY DIFFRACTION2.59120
25FW2|1|A+ 5FW2|1|C+ 5FW2|1|DCrystal structure of SpCas9 variant EQR bound to sgRNA and TGAG PAM target DNAX-RAY DIFFRACTION2.68120
35FW3|1|A+ 5FW3|1|C+ 5FW3|1|DCrystal structure of SpCas9 variant VRER bound to sgRNA and TGCG PAM target DNAX-RAY DIFFRACTION2.7120
45FW1|1|A+ 5FW1|1|C+ 5FW1|1|DCrystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNAX-RAY DIFFRACTION2.5120
54UN4|1|A+ 4UN4|1|ECrystal structure of Cas9 bound to PAM-containing DNA target with mismatches at positions 1-2X-RAY DIFFRACTION2.3799
65FQ5|1|A+ 5FQ5|1|ECrystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasingX-RAY DIFFRACTION2.14100
74UN5|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.

4UN3|1|A+4UN3|1|C+4UN3|1|D:4UN3|1|A+4UN3|1|C+4UN3|1|D = 04UN3|1|A+4UN3|1|C+4UN3|1|D:5FW2|1|A+5FW2|1|C+5FW2|1|D = 0.02774UN3|1|A+4UN3|1|C+4UN3|1|D:5FW3|1|A+5FW3|1|C+5FW3|1|D = 0.03024UN3|1|A+4UN3|1|C+4UN3|1|D:5FW1|1|A+5FW1|1|C+5FW1|1|D = 0.04194UN3|1|A+4UN3|1|C+4UN3|1|D:4UN4|1|A+4UN4|1|E = 0.14314UN3|1|A+4UN3|1|C+4UN3|1|D:5FQ5|1|A+5FQ5|1|E = 0.14704UN3|1|A+4UN3|1|C+4UN3|1|D:4UN5|1|A+4UN5|1|E = 0.15445FW2|1|A+5FW2|1|C+5FW2|1|D:4UN3|1|A+4UN3|1|C+4UN3|1|D = 0.02775FW2|1|A+5FW2|1|C+5FW2|1|D:5FW2|1|A+5FW2|1|C+5FW2|1|D = 05FW2|1|A+5FW2|1|C+5FW2|1|D:5FW3|1|A+5FW3|1|C+5FW3|1|D = 0.02405FW2|1|A+5FW2|1|C+5FW2|1|D:5FW1|1|A+5FW1|1|C+5FW1|1|D = 0.04305FW2|1|A+5FW2|1|C+5FW2|1|D:4UN4|1|A+4UN4|1|E = 0.14275FW2|1|A+5FW2|1|C+5FW2|1|D:5FQ5|1|A+5FQ5|1|E = 0.14555FW2|1|A+5FW2|1|C+5FW2|1|D:4UN5|1|A+4UN5|1|E = 0.15235FW3|1|A+5FW3|1|C+5FW3|1|D:4UN3|1|A+4UN3|1|C+4UN3|1|D = 0.03025FW3|1|A+5FW3|1|C+5FW3|1|D:5FW2|1|A+5FW2|1|C+5FW2|1|D = 0.02405FW3|1|A+5FW3|1|C+5FW3|1|D:5FW3|1|A+5FW3|1|C+5FW3|1|D = 05FW3|1|A+5FW3|1|C+5FW3|1|D:5FW1|1|A+5FW1|1|C+5FW1|1|D = 0.03695FW3|1|A+5FW3|1|C+5FW3|1|D:4UN4|1|A+4UN4|1|E = 0.14285FW3|1|A+5FW3|1|C+5FW3|1|D:5FQ5|1|A+5FQ5|1|E = 0.14645FW3|1|A+5FW3|1|C+5FW3|1|D:4UN5|1|A+4UN5|1|E = 0.15315FW1|1|A+5FW1|1|C+5FW1|1|D:4UN3|1|A+4UN3|1|C+4UN3|1|D = 0.04195FW1|1|A+5FW1|1|C+5FW1|1|D:5FW2|1|A+5FW2|1|C+5FW2|1|D = 0.04305FW1|1|A+5FW1|1|C+5FW1|1|D:5FW3|1|A+5FW3|1|C+5FW3|1|D = 0.03695FW1|1|A+5FW1|1|C+5FW1|1|D:5FW1|1|A+5FW1|1|C+5FW1|1|D = 05FW1|1|A+5FW1|1|C+5FW1|1|D:4UN4|1|A+4UN4|1|E = 0.13385FW1|1|A+5FW1|1|C+5FW1|1|D:5FQ5|1|A+5FQ5|1|E = 0.13745FW1|1|A+5FW1|1|C+5FW1|1|D:4UN5|1|A+4UN5|1|E = 0.14594UN4|1|A+4UN4|1|E:4UN3|1|A+4UN3|1|C+4UN3|1|D = 0.14314UN4|1|A+4UN4|1|E:5FW2|1|A+5FW2|1|C+5FW2|1|D = 0.14274UN4|1|A+4UN4|1|E:5FW3|1|A+5FW3|1|C+5FW3|1|D = 0.14284UN4|1|A+4UN4|1|E:5FW1|1|A+5FW1|1|C+5FW1|1|D = 0.13384UN4|1|A+4UN4|1|E:4UN4|1|A+4UN4|1|E = 04UN4|1|A+4UN4|1|E:5FQ5|1|A+5FQ5|1|E = 0.02664UN4|1|A+4UN4|1|E:4UN5|1|A+4UN5|1|E = 0.05445FQ5|1|A+5FQ5|1|E:4UN3|1|A+4UN3|1|C+4UN3|1|D = 0.14705FQ5|1|A+5FQ5|1|E:5FW2|1|A+5FW2|1|C+5FW2|1|D = 0.14555FQ5|1|A+5FQ5|1|E:5FW3|1|A+5FW3|1|C+5FW3|1|D = 0.14645FQ5|1|A+5FQ5|1|E:5FW1|1|A+5FW1|1|C+5FW1|1|D = 0.13745FQ5|1|A+5FQ5|1|E:4UN4|1|A+4UN4|1|E = 0.02665FQ5|1|A+5FQ5|1|E:5FQ5|1|A+5FQ5|1|E = 05FQ5|1|A+5FQ5|1|E:4UN5|1|A+4UN5|1|E = 0.04564UN5|1|A+4UN5|1|E:4UN3|1|A+4UN3|1|C+4UN3|1|D = 0.15444UN5|1|A+4UN5|1|E:5FW2|1|A+5FW2|1|C+5FW2|1|D = 0.15234UN5|1|A+4UN5|1|E:5FW3|1|A+5FW3|1|C+5FW3|1|D = 0.15314UN5|1|A+4UN5|1|E:5FW1|1|A+5FW1|1|C+5FW1|1|D = 0.14594UN5|1|A+4UN5|1|E:4UN4|1|A+4UN4|1|E = 0.05444UN5|1|A+4UN5|1|E:5FQ5|1|A+5FQ5|1|E = 0.04564UN5|1|A+4UN5|1|E:4UN5|1|A+4UN5|1|E = 04UN3|1|A+4UN3|1|C+4UN3|1|D5FW2|1|A+5FW2|1|C+5FW2|1|D5FW3|1|A+5FW3|1|C+5FW3|1|D5FW1|1|A+5FW1|1|C+5FW1|1|D4UN4|1|A+4UN4|1|E5FQ5|1|A+5FQ5|1|E4UN5|1|A+4UN5|1|EDiscrepancy0.000.020.040.060.080.100.120.14

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