Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in partial R-loop state

2026-02-11 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBj PDBj 2025-07-11 2026-02-11 2026-02-11 2026-02-11 Japan Society for the Promotion of Science (JSPS) 20H02916 Japan Japan Society for the Promotion of Science (JSPS) 24H00505 Japan Japan Society for the Promotion of Science (JSPS) 23KJ1734 Japan Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in partial R-loop state Ishihara K Numata T CRISPR-associated transposon, DNA BINDING PROTEIN Ishihara K Matsumoto S Gerle C Gopalasingam CC Shigematsu H Shirai T Numata T Sequential structural rearrangements at the PAM-distal site of a type I-F3 CRISPR-Cas effector enabling RNA-guided DNA transposition. Nucleic Acids Res. UK 54 2026 41495894 doi:10.1093/nar/gkaf1415 1362-4962 0389 NARHAD 9vtp FULLOVERLAP EMDB EMD-65338 associated EM volume

Vibrio parahaemolyticus type I-F3 TniQ-Cascade Vibrio parahaemolyticus type I-F3 TniQ-Cascade 0 1 2 3 4 6 7 Vibrio parahaemolyticus RIMD 2210633 0.494 crRNA from Vibrio parahaemolyticus Vibrio parahaemolyticus RIMD 2210633 0.019405658 1 CUGAUAAUGAGAUACCACAAGCUCAAGCAGAUGCUAACAGGUGAACUGCCGAAUAGGUAG BA000032.2 Target strand DNA from Vibrio alginolyticus K08M03 plasmid pL300 Vibrio alginolyticus 0.023027675999999997 1 (DC)(DA)(DG)(DC)(DC)(DG)(DC)(DT)(DT)(DC)(DA)(DT)(DC)(DA)(DT)(DT)(DC)(DA)(DG)(DC) (DC)(DT)(DG)(DT)(DT)(DA)(DG)(DC)(DA)(DT)(DC)(DT)(DG)(DC)(DT)(DT)(DG)(DA)(DG)(DC) (DC)(DT)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DT)(DA) (DC)(DG)(DT)(DA)(DA)(DG)(DA)(DC)(DT)(DC)(DT)(DG)(DC)(DT)(DT) CP017915.1 DNA Non-target strand DNA from Vibrio alginolyticus strain K08M3 plasmid pL300 Vibrio alginolyticus 0.023224912 1 (DA)(DA)(DG)(DC)(DA)(DG)(DA)(DG)(DT)(DC)(DT)(DT)(DA)(DC)(DG)(DT)(DA)(DA)(DA)(DC) (DA)(DC)(DC)(DC)(DG)(DG)(DA)(DT)(DA)(DC)(DC)(DA)(DC)(DA)(DG)(DG)(DC)(DT)(DC)(DA) (DA)(DG)(DC)(DA)(DG)(DA)(DT)(DG)(DC)(DT)(DA)(DA)(DC)(DA)(DG)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DG)(DA)(DT)(DG)(DA)(DA)(DG)(DC)(DG)(DG)(DC)(DT)(DG) CP017915.1 DNA Type I-F CRISPR-associated protein Csy3 Vibrio parahaemolyticus RIMD 2210633 0.039455413999999994 6 Escherichia coli BL21(DE3) LEVO MKLPNGLSYMKSIEASDVIFLVNWPDGRKTPLPYTSRVALGMKEGSKSAYKYDGQIDADVTAYSLAQGNPHEIDFCCVPY GAESIECEFSVSFASSLRKPFKCSDPEVKRTLVQLIKLYEEKVGWEELANRFLENICNGRWLWRNNECTYSTSIGIKPWP WEDEKAISPFHDIRKNYAGTNHFRDHKDWDNLIKLITDAFSQPNGLCIFEVSATFRLGTNAPIYPSQVFKDSVKGEKNRI YQSTDVDGESSPILGCYKTGAAIATIDDWYPDADKPIRISHYGAHREDVYCYRHPNTGKDLFTLLEKADQYLEQLQATDV LPDEMINDLHFIVANLIKGGLLQQKGT Q87GC8 CRISPR-associated protein Csy2 Vibrio parahaemolyticus RIMD 2210633 0.071108406

Chain g corresponds to an unassignable region of the Cas8/5 helical bundle in chain G (residues 326-389).

1 Escherichia coli BL21(DE3) LEVO MATLAEILDNKTDDLNKDLRRAFRPLSAPVDISDTPIEALTILVNLTDRVIEQKNLLDRQKCKDKLRDEKWWANCFRTVK YRQSHNPKFPDIRANGVIRAAPVGHLPACMLSSSKLPQNSWAYANDSSQMNKSCFLTSEFIWNGDVHCLGQLLTELEHPL WNVLRKLGCYVKTAKYISKELALIPPLEINTSLVRNYLAQISLPNNEDSYISLSPVVSQSMQEDCYQVLSEHYRFSAITR FSRATNMGTLAMSCGGKFKMIRSLPPIEKYQHHHLDSVNWLTKRSVRAIRDYTESSVWVISPNKLALRKKSIIGDIKMML SQWLR(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)KYLLLPNLRISGASAMNTSVSIGIPSMMAFYGFVHAFQRNVQTANPNFKIESFAVCIHNIHVENRGLTREWVPNT KGQITAPATRDDWQCDVAVSLILRCSHYSQLIPRDFIRLLPGRIARGKVTVSISDIKHLGRCLSLADAIKAIPVETGRWL SLNNEVTLNSIQDVIDELKNNKLQTVNCIGYHRLETPCEKRGSLHGYKHAFVETILGIIKFLTISENTNPSQYFWQYHYS KQGPILLPRSVSDETS Q87GC9 CRISPR-associated protein, Csy4 family Vibrio parahaemolyticus RIMD 2210633 0.022919 1 Escherichia coli BL21(DE3) LEVO MDWHYRTITFLPEYRNNEAIAAKCIKELHRFNYKYETRSIGVSFPLWGQETVGRKITFVSTNKMELDFLISRRYFVQMTK LGYFSISTTQTVPDDCSYVLFKRAHSIDKGTFAGRARELKRLERRALERGEIFDPIAYSKTTSHAFQSYHSLEEDSSSGN KFRLNIQMKERSGTVGTGKFSSYGLGNTDNSLQVVPLI Q87GC7 TniQ Vibrio parahaemolyticus RIMD 2210633 0.04735711299999999 2 Escherichia coli BL21(DE3) LEVO GPRISEFMVQMMLLQRPKSYPDESLESFFIRVANKNGYNDVHWFLVAVKRYLLDIDPRKFQTFPTDICCINPYSSKKHSI SRTHALHHLSQLTFNEPVDLLGIALNRNQMQFSPSTTALIRGAEVIPRSLLRKGAIPCCPCCLGEHGYASYRWHFSGYEY CHEHDVKLIERCSCGAIYDYRYAGLSGVCTECGENISASQENHEPKATRIASWLAGDDVKPLPDVPLSYRWGFMHWWSQI SSSCKTRNNGEFLAFWEHWPNSFHKLIGKEIDFNFEYCVLSKNDLRVKDILGKILFSSIQLPDRNFRSNIILKEMFQYIE THLWDDNGKLANLRMNMLEICVLLNCSREQVTSMIEQGLLPPNRQLGKREILIVTEYAFYLGDVYCLWLSEFQSDEFNRS FYLSRW Q87GD0 MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 2.00 7.4 20.0 Tris-HCl 100.0 NaCl 1.0 DTT 5.0 MgCl2 0.001 LMNG Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY ARRAY GLOW DISCHARGE 10 AIR 0.007 ETHANE 100 281 FEI VITROBOT MARK IV JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.4000000000000001 1.6 60000.0 NITROGEN In-column Omega Filter GATAN K3 BIOCONTINUUM (6k x 4k) 4906 50.31 1 C1 2.68 31509 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 4 15364.0 emd_65338.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 345.91998 345.91998 345.91998 90.0 90.0 90.0 X Y Z -0.6913914 1.9250482 0.00014829008 0.047161225 0.752 0.752 0.752 0.16 AUTHOR ::::EMDATABANK.org::::EMD-65338:::: Primary map SwissModel in silico model AlphaFold in silico model emd_65338_msk_1.map emd_65338_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 345.91998 345.91998 345.91998 90.0 90.0 90.0 X Y Z -1.8940023 4.2066875 0.00014829011 0.099984564 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-65338:::: Sharpened map from Non-Uniform Refinement emd_65338_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 345.91998 345.91998 345.91998 90.0 90.0 90.0 X Y Z -0.0043554488 1.9115831 0.0010869337 0.024769317 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-65338:::: Focused map from Local Refinement sharpened using DeepEMhancer emd_65338_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 345.91998 345.91998 345.91998 90.0 90.0 90.0 X Y Z -2.6147733 3.597026 0.00089960574 0.29120407 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-65338:::: Half map 2 emd_65338_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 345.91998 345.91998 345.91998 90.0 90.0 90.0 X Y Z -2.1432686 3.0763972 0.000892676 0.28830048 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-65338:::: Half map 1