RNA 3D Hub //

Equivalence class NR_3.0_56990.5 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
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
58SRS|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
66AI6|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
74OO8|1|B+ 4OO8|1|CTrans-activating crRNADNA (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
87S4X|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
97Z4J|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
104OO8|1|E+ 4OO8|1|FTrans-activating crRNADNA (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
119ED9|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
129EAL|1|B+ 9EAL|1|C+ 9EAL|1|DTrans-activating crRNADNA (Non-target strand), DNA (Target Strand), sgRNAsynthetic constructSyntheticRF02348SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State II - precleavage)Electron microscopy2.831432025-07-09
139EAK|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
148YE6|1|CTrans-activating crRNARNA (92-MER)Streptococcus pyogenesBacteriaRF02348Cryo-EM structure of Cas9-sgRNA-A32 complexElectron microscopy2.95922024-09-11
158T6Y|1|BTrans-activating crRNAgRNAStreptococcus pyogenesBacteriaRF02348SpRY-Cas9:gRNA complex bound to non-target DNA with 1 bp R-loopElectron microscopy2.88882024-05-01
169EDA|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
179CGU|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
184ZT0|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
199JL2|1|B+ 9JL2|1|C+ 9JL2|1|DTrans-activating crRNAgRNA, NTS, TSunclassified sequencesRF02348Classical conformation for the spCas9 with gRNA and target DNA complexElectron microscopy31342025-09-24
204ZT0|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

Release history

Release4.6
Date2025-09-24

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
14OO8|1|E+ 4OO8|1|FCrystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-RAY DIFFRACTION2.5120
25B2S|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
35B2R|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
45B2T|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
56AI6|1|B+ 6AI6|1|C+ 6AI6|1|DCrystal structure of SpCas9-NGX-RAY DIFFRACTION2.7117
64OO8|1|B+ 4OO8|1|CCrystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNAX-RAY DIFFRACTION2.5118
79CGU|1|B+ 9CGU|1|C+ 9CGU|1|DCas9 ternary complex, 14-nt sgRNA, State II (kinked)ELECTRON MICROSCOPY3144
89EAK|1|B+ 9EAK|1|C+ 9EAK|1|DSpCas9 with 17-bp R-loop containing 2 terminal mismatches (State I - pre-activation)ELECTRON MICROSCOPY2.76149
99EAL|1|B+ 9EAL|1|C+ 9EAL|1|DSpCas9 with 17-bp R-loop containing 2 terminal mismatches (State II - precleavage)ELECTRON MICROSCOPY2.83143
109ED9|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
119EDA|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
127Z4L|1|A+ 7Z4L|1|C+ 7Z4L|1|DSpCas9 bound to 18-nucleotide complementary DNA substrate in the checkpoint stateELECTRON MICROSCOPY2.54136
139JL2|1|B+ 9JL2|1|C+ 9JL2|1|DClassical conformation for the spCas9 with gRNA and target DNA complexELECTRON MICROSCOPY3134
147S4X|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
157Z4J|1|A+ 7Z4J|1|D+ 7Z4J|1|C+ 7Z4J|1|cSpCas9 bound to 18-nucleotide complementary DNA substrate in the catalytic stateELECTRON MICROSCOPY2.99142
168SRS|1|B+ 8SRS|1|D+ 8SRS|1|c+ 8SRS|1|CSpRY-Cas9:gRNA complex targeting TAC PAM DNAELECTRON MICROSCOPY2.79149
178T6Y|1|BSpRY-Cas9:gRNA complex bound to non-target DNA with 1 bp R-loopELECTRON MICROSCOPY2.8888
188YE6|1|CCryo-EM structure of Cas9-sgRNA-A32 complexELECTRON MICROSCOPY2.9592
194ZT0|1|DCrystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolutionX-RAY DIFFRACTION2.972
204ZT0|1|BCrystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolutionX-RAY DIFFRACTION2.972

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 0.0114 s