Cryo-EM structure of a type II-D CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA

2025-08-20 REL PDBc INITIAL_RELEASE REPOSITORY PDBj PDBc 2025-01-10 2025-08-20 2025-08-20 2025-08-20 National Natural Science Foundation of China (NSFC) China Cryo-EM structure of a type II-D CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA Wang K Wang Y Complex, CRISPR, HYDROLASE Wang K Wang J Yang X Sun W Sheng G Wang Y Structural insights into Type II-D Cas9 and its robust cleavage activity. Nat Commun UK 16 7396 7396 2025 40790018 doi:10.1038/s41467-025-62128-8 2041-1723 9lgi FULLOVERLAP EMDB EMD-63066 associated EM volume

Ternary complex of NsCas9-sgRNA-dsDNA Ternary complex of NsCas9-sgRNA-dsDNA 0 1 2 3 4 Nitrospirae bacterium RBG_13_39_12 HNH nuclease domain-containing protein Nitrospirae bacterium RBG_13_39_12 0.088439391 1 Escherichia coli LEVO MEKELVLGIDYGGKYTGLAVVNQKNNQVLYARTVKMRDDVTDILAGRREQRSLRRTLQTKKKRLRELKNYLESIGGIYEE SSGTFTIEPFRTVYSLAHKRGYDYADLPEEKTSEEIEAMDAKERKQWEKEKKELEETQRNSRHRDEVLRDVRNVMTEGNL SEEQIIKVESIFNKQYRHKRFNNRILTKCKVCGKNTPLRINVRELLLENIVRYLPLQNKERELLKLTILKGHQQDINEIF KHFRKVYKITLNQKDWPGKNLIDIARNQLRGRLLFCKVHFPENEKYVSIEKKTFRLAPSLKTKIENVLSVIKDDILPNFT LNNVVMESNNFDIAAKTKGKKRLLKEEYSKGHRESGETRKEALLRETDSRCIYCGKGIDLSNAHEDHIFPRKAGGINIFG NLVACCSVCNEEKRGRTPLESGILPKPEIVSFITNDLKKKILEDAQYINTLDFNKYMSHASIGWRHMRDRLRELTGNKEL LIKRQSGIYTAYFRKWWGFIKERGNHGHHALDAVILASKKSYAEDGKVDMTIKPCGEDGKEFDIERHLSEMKEFRRDKGG KSAPLHDRNPLSFKNDIITRRFMVTEIECGKEAVIISEEYRKKLTEAFKRFGIAKGKYLTDEQAKDAGFYLRKNGEGVMS LKCEVKGTGYNQMIRIKNNIFKTNVHNVGVAVFLDEKGKKRACELKNPRLSKHFVKPAEQVKGKVIFILKRGNMVTVEGE EMIYRVKKLGTSPVIEAIVGSDGKTRTVSATKLLKINHTKKV A0A1G1G089 sgRNA (156-MER) Nitrospirae bacterium RBG_13_39_12 0.05021164499999999 1 GGUUAUAACUGAUAUAUGGGGUUACAGUUAAGGCUCUUUGAAAAAAGAGCCUUAAUUGUAAAACGCCUAUACGGUGAGGG UAUGUACGUUUGGGUUUGUCCAGCCUAAACCUCUACGCCAGAAAUGGCACCUUCAUUGUGGGUUAGGACAAUUUAA DNA (41-MER) synthetic construct 0.012489061 1 (DT)(DC)(DT)(DA)(DG)(DA)(DG)(DG)(DA)(DT)(DC)(DC)(DC)(DC)(DC)(DC)(DA)(DT)(DA)(DT) (DA)(DT)(DC)(DA)(DG)(DT)(DT)(DA)(DT)(DA)(DA)(DC)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DA) (DC) DNA DNA (41-MER) synthetic construct 0.012560096 1 (DG)(DT)(DG)(DA)(DA)(DT)(DT)(DC)(DC)(DC)(DA)(DA)(DT)(DA)(DT)(DT)(DG)(DA)(DC)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DC)(DC)(DG)(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DA)(DG) (DA) DNA ZINC ION 6.5409e-05 2 ZN water 1.8015e-05 6 HOH singleParticle particle 7.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 1.4000000000000001 GATAN K2 QUANTUM (4k x 4k) 60.0 1 NONE 2.86 FSC 0.143 CUT-OFF 215731 PROJECTION MATCHING ANGULAR RECONSTITUTION emd_63066.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 246.0 246.0 246.0 90.0 90.0 90.0 X Y Z -0.25915954 0.51986295 -0.00050221354 0.012588706 0.82 0.82 0.82 0.04 AUTHOR ::::EMDATABANK.org::::EMD-63066:::: emd_63066_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 246.0 246.0 246.0 90.0 90.0 90.0 X Y Z -0.3363768 0.62382424 0.00015718745 0.024799004 0.82 0.82 0.82 AUTHOR ::::EMDATABANK.org::::EMD-63066:::: emd_63066_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 246.0 246.0 246.0 90.0 90.0 90.0 X Y Z -0.3337033 0.6235909 0.00014744919 0.024846073 0.82 0.82 0.82 AUTHOR ::::EMDATABANK.org::::EMD-63066::::