2025-05-14 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2024-02-29 2025-01-15 2025-01-15 2025-05-14 Welch Foundation F-1938 United States Cas9d 20bp R-loop Complex Fregoso Ocampo R Taylor DW Bravo JPK DNA/RNA CRISPR Cas9 Cas9d Nuclease sgRNA, DNA BINDING PROTEIN, RNA BINDING PROTEIN-DNA-RNA complex Ocampo RF Bravo JPK Dangerfield TL Nocedal I Jirde SA Alexander LM Thomas NC Das A Nielson S Johnson KA Brown CT Butterfield CN Goltsman DSA Taylor DW DNA targeting by compact Cas9d and its resurrected ancestor. Nat Commun UK 16 457 457 2025 39774105 doi:10.1038/s41467-024-55573-4 2041-1723 9auf FULLOVERLAP Cas9d ternary complex with a 20bp R-loop Cas9d ternary complex with a 20bp R-loop 0 1 2 3 4 5 Deltaproteobacteria 0.171 HNH nuclease domain-containing protein Deltaproteobacteria 0.086696844 1 Escherichia coli LEVO MERELVLGIDYGGKYTGLAVVDRRHNQVLYANRLKMRDDVAGILKDRRKQRGIRRTAQTKKKRLRELKNYLKSIGYNEST ATFETVYSLAHKRGYDYADMPEEKTSEEIEAMDVEERKQWEKEKQEWEETKRNSRHRKEVVKDVHKAMIEGRATEEQIKR VERIFNKQYRPKRFNNRILTKCKVEDCGVNTPLRKNVRDLLIENIVRFFPIEQSEKDNLKDAVLDKNRREEVKSFFRKHK TDEHIRKQVYDIADNKLSGRTVFCKEHILEHTEHSKEERKVFRLAPSLKTKIENVLAVIKDEILPKFTVNKVVMESNNFD IAAKTQGKKRLAKEEYGKGPREGKETRKEALLRETDGRCIYCGKSIDISNAHDDHIFPRKAGGLNIFANLVACCAVCNEN KKGRTPLESGISPKPEIIAFMKNDLKKKILEDARNINTVDFNKYMSHASIGWRYMRDRLRESAGNKKLPIERQSGIYTAY FRRWWGFKKERGNTLHHALDAVILASRKGYSDDGLVDMTLKPKYNKGGEFDPEKHLPEPIEFKMDKGSRGSALHDRNPLS YKKGIITRRFMVTEIECGKEDDVISETYREKLKEAFKRFDTKKGKCLTDKEAKEAGFCIKKNELVMSLKCSIKGTGPGQM IRINNNVFKTNVHNVGVDVYLDEKGKKKAYERKNPRLSKHFIEPPPQPNGRVSFTLKRRDMVTVEGEDAIYRIKKLGTSP TIEAVVGSDGKTRTVSATKLTKANSAE A0A1F8ZSN4 sgRNA Deltaproteobacteria 0.050836031000000004 1 GACGCAUAAAGAUGAGACGCGUUACAGUUAAGGCUCUGAAAAGAGCCUUAAUUGUAAAACGCCUAUACAGUGAAGGGAUA UACGCUUGGGUUUGUCCAGCCUGAGCCUCUAUGCCAGAAAUGGCGCCUUCAUCGUGGGUUAGGACAUUUAAUUUUUUU 5' Target Strand Deltaproteobacteria 0.006743351999999999 1 (DA)(DG)(DC)(DT)(DG)(DA)(DC)(DG)(DT)(DT)(DT)(DG)(DT)(DA)(DC)(DT)(DC)(DC)(DA)(DG) (DC)(DG) DNA Non-Target Strand Deltaproteobacteria 0.017026958999999998 1 (DA)(DG)(DC)(DA)(DG)(DA)(DA)(DA)(DT)(DC)(DT)(DC)(DT)(DG)(DC)(DT)(DG)(DA)(DC)(DG) (DC)(DA)(DT)(DA)(DA)(DA)(DG)(DA)(DT)(DG)(DA)(DG)(DA)(DC)(DG)(DC)(DT)(DG)(DG)(DA) (DG)(DT)(DA)(DC)(DA)(DA)(DA)(DC)(DG)(DT)(DC)(DA)(DG)(DC)(DT) DNA 3' Target Strand Deltaproteobacteria 0.010077478999999999 1 (DT)(DC)(DT)(DC)(DA)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DG)(DC)(DG)(DT)(DC)(DA)(DG)(DC) (DA)(DG)(DA)(DG)(DA)(DT)(DT)(DT)(DC)(DT)(DG)(DC)(DT) DNA singleParticle particle 7.9 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 2.5 GATAN K3 (6k x 4k) 80.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.73 FSC 0.143 CUT-OFF 1164607 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_43878.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 319.9488 319.9488 319.9488 90.0 90.0 90.0 X Y Z -6.3181453 9.720691 -0.00028394145 0.112122186 0.8332 0.8332 0.8332 0.649 AUTHOR Cas9d 20bp R-loop Complex emd_43878_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 319.9488 319.9488 319.9488 90.0 90.0 90.0 X Y Z -0.33445823 1.4115613 -0.00028394142 0.028338747 0.8332 0.8332 0.8332 AUTHOR Additional Map emd_43878_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 319.9488 319.9488 319.9488 90.0 90.0 90.0 X Y Z -0.35472432 1.464585 0.0002456767 0.030405942 0.8332 0.8332 0.8332 AUTHOR Half Map A emd_43878_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 319.9488 319.9488 319.9488 90.0 90.0 90.0 X Y Z -0.34421363 1.4601116 0.00023816118 0.030400893 0.8332 0.8332 0.8332 AUTHOR Half Map B