2023-11-22 REL RCSB RCSB RCSB 2022-12-21 2023-09-06 2023-09-06 2023-11-22 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM147842 United States Life Sciences Research Foundation Simons Foundation United States M.J. Murdock Charitable Trust National Science Foundation (NSF, United States) 1828765 United States NIH Common Fund Transformative High Resolution Cryo-Electron Microscopy program GM129539 Simons Foundation SF349247 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM134867 United States Amgen Montana State University Agricultural Experimental Station (USDA NIFA) VIRIS Detection Systems Santiago-Frangos A Henriques WS Wiegand T Gauvin C Buyukyoruk M Neselu K Eng ET Lander GC Wiedenheft B DNA integration, maintenance of CRISPR repeat elements, IHF-DNA complex, Enzymes altering nucleic acid conformation, Site specific endodeoxyribonucleases: cleavage is not sequence specific, Nucleotidyltransferases, GO:0008301, RECOMBINATION, DNA BINDING PROTEIN, HYDROLASE-DNA complex Santiago-Frangos A Henriques WS Wiegand T Gauvin CC Buyukyoruk M Graham AB Wilkinson RA Triem L Neselu K Eng ET Lander GC Wiedenheft B Nat.Struct.Mol.Biol. US 30 1675 1685 2023 37710013 doi:10.1038/s41594-023-01097-2 1545-9985 8flj FULLOVERLAP Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA 0 1 2 3 4 5 6 7 8 .122 Cas1-Cas2/3 heterohexameric integrase 1 1 8 Pseudomonas aeruginosa PA14 IHF heterodimer 1 2 3 Pseudomonas aeruginosa PA14 CRISPR leader, repeat, and prespacer DNA annealed to mimic a half-site integration intermediate. 1 4 5 6 7 CRISPR-associated endonuclease Cas1 Pseudomonas aeruginosa PA14 0.038267148 4 Escherichia coli BL21(DE3) LEVO MWSHPQFEKENLYFQGSMDDISPSELKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTG TSITQAAMRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLER IRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPAN RFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAMRGDEEQDFRQACLDNLSRA QALDFMIDTLKDVAQRSTVSA Q02ML7 3.1.-.- Integration host factor subunit alpha Pseudomonas aeruginosa PA14 0.011646299 2 Escherichia coli BL21(DE3) LEVO GPMGALTKAEIAERLYEELGLNKREAKELVELFFEEIRQALEHNEQVKLSGFGNFDLRDKRQRPGRNPKTGEEIPITARR VVTFRPGQKLKARVEAYAGTKS Q02NN5 Integration host factor subunit beta Pseudomonas aeruginosa PA14 0.010805378000000001 2 Escherichia coli BL21(DE3) LEVO GPMTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVP HFKPGKELRDRVNEPE Q02PW7 CRISPR leader, sense strand of DNA Pseudomonas aeruginosa PA14 0.042935559 1 (DA)(DA)(DG)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DC)(DC)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DC) (DG)(DG)(DA)(DC)(DG)(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DA)(DA)(DA)(DC)(DC)(DC)(DT)(DT) (DA)(DT)(DA)(DA)(DA)(DT)(DC)(DA)(DG)(DC)(DA)(DA)(DG)(DT)(DT)(DA)(DC)(DG)(DA)(DG) (DA)(DC)(DC)(DT)(DC)(DG)(DA)(DA)(DA)(DA)(DA)(DA)(DG)(DA)(DG)(DG)(DG)(DT)(DT)(DT) (DC)(DT)(DG)(DG)(DC)(DG)(DG)(DG)(DA)(DA)(DA)(DA)(DA)(DC)(DT)(DC)(DA)(DA)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DT)(DT)(DC)(DG)(DA)(DA)(DA)(DT)(DC)(DA)(DA)(DC)(DC)(DG)(DG) (DT)(DT)(DA)(DT)(DA)(DG)(DG)(DT)(DT)(DT)(DT)(DC)(DG)(DG)(DA)(DG)(DC)(DT)(DA) DNA CRISPR leader and repeat, anti-sense strand of DNA Pseudomonas aeruginosa PA14 0.05270164499999999 1 (DT)(DG)(DA)(DT)(DT)(DT)(DT)(DC)(DT)(DT)(DA)(DG)(DC)(DT)(DG)(DC)(DC)(DT)(DA)(DC) (DA)(DC)(DG)(DG)(DC)(DA)(DG)(DT)(DG)(DA)(DA)(DC)(DT)(DA)(DG)(DC)(DT)(DC)(DC)(DG) (DA)(DA)(DA)(DA)(DC)(DC)(DT)(DA)(DT)(DA)(DA)(DC)(DC)(DG)(DG)(DT)(DT)(DG)(DA)(DT) (DT)(DT)(DC)(DG)(DA)(DA)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DA)(DG)(DT)(DT) (DT)(DT)(DT)(DC)(DC)(DC)(DG)(DC)(DC)(DA)(DG)(DA)(DA)(DA)(DC)(DC)(DC)(DT)(DC)(DT) (DT)(DT)(DT)(DT)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DC)(DT)(DC)(DG)(DT)(DA)(DA)(DC)(DT) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DT)(DT)(DA)(DT)(DA)(DA)(DG)(DG)(DG)(DT)(DT)(DT)(DT) (DT)(DT)(DA)(DA)(DA)(DT)(DC)(DG)(DT)(DC)(DC)(DG)(DA)(DA)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DT)(DC)(DG)(DG)(DA)(DA)(DG)(DC)(DT)(DT) DNA CRISPR repeat and prespacer, sense strand of DNA synthetic construct 0.018241707 1 (DG)(DT)(DG)(DC)(DA)(DA)(DG)(DT)(DC)(DG)(DT)(DT)(DT)(DT)(DG)(DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DA)(DC)(DA)(DT)(DG)(DT)(DT)(DC)(DA)(DC)(DT)(DG)(DC)(DC)(DG)(DT)(DG) (DT)(DA)(DG)(DG)(DC)(DA)(DG)(DC)(DT)(DA)(DA)(DG)(DA)(DA)(DA)(DA)(DT)(DC)(DA) DNA Prespacer, anti-sense strand of DNA synthetic construct 0.008263363999999999 1 (DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DA)(DA)(DA)(DC)(DG)(DA)(DC)(DT)(DT)(DG)(DC) (DA)(DC)(DA)(DA)(DC)(DG)(DA) DNA CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST Pseudomonas aeruginosa PA14 0.12127367999999998 2 Escherichia coli BL21(DE3) LEVO MNILLVSQCEKRALSETRRILDQFAERRGERTWQTPITQAGLDTLRRLLKKSARRNTAVACHWIRGRDHSELLWIVGDAS RFNAQGAVPTNRTCRDILRKEDENDWHSAEDIRLLTVMAALFHDIGKASQAFQAKLRNRGKPMADAYRHEWVSLRLFEAF VGPGSSDEDWLRRLADKRETGDAWLSQLARDDRQSAPPGPFQKSRLPPLAQAVGWLIVSHHRLPNGDHRGSASLARLPAP IQSQWCGARDADAKEKAACWQFPHGLPFASAHWRARTALCAQSMLERPGLLARGPALLHDSYVMHVSRLILMLADHHYSS LPADSRLGDPNFPLHANTDRDSGKLKQRLDEHLLGVALHSRKLAGTLPRLERQLPRLARHKGFTRRVEQPRFRWQDKAYD CAMACREQAMEHGFFGLNLASTGCGKTLANGRILYALADPQRGARFSIALGLRSLTLQTGQAYRERLGLGDDDLAILVGG SAARELFEKQQERLERSGSESAQELLAENSHVHFAGTLEDGPLREWLGRNSAGNRLLQAPILACTIDHLMPASESLRGGH QIAPLLRLMTSDLVLDEVDDFDIDDLPALSRLVHWAGLFGSRVLLSSATLPPALVQGLFEAYRSGREIFQRHRGAPGRAT EIRCAWFDEFSSQSSAHGAVTSFSEAHATFVAQRLAKLEQLPPRRQAQLCTVHAAGEARPALCRELAGQMNTWMADLHRC HHTEHQGRRISFGLLRLANIEPLIELAQAILAQGAPEGLHVHLCVYHSRHPLLVRSAIERQLDELLKRSDDDAAALFARP TLAKALQASTERDHLFVVLASPVAEVGRDHDYDWAIVEPSSMRSIIQLAGRIRRHRSGFSGEANLYLLSRNIRSLEGQNP AFQRPGFETPDFPLDSHDLHDLLDPALLARIDASPRIVEPFPLFPRSRLVDLEHRRLRALMLADDPPSSLLGVPLWWQTP ASLSGALQTSQPFRAGAKERCYALLPDEDDEERLHFSRYEEGTWSNQDNLLRNLDLTYGPRIQTWGTVNYREELVAMAGR EDLDLRQCAMRYGEVRLRENTQGWSYHPYLGFKKYN Q02ML8 3.1.-.- singleParticle particle 7.5 20.0 Tris-HCl 200.0 Monopotassium glutamate 5.0 EDTA 1.0 TCEP 0.2 Glycerol Quantifoil R2/2 COPPER 200 GLOW DISCHARGE 15

Grids were glow discharged at 15 mA for 15 seconds with a 10 second hold (easiGlow, Pelco).

ETHANE 100 281.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.7000000000000001 2.1 81000.0 46860.0 20 GATAN K3 BIOQUANTUM (6k x 4k) 11520 8184 10740 2.5 69.0 1

Patch motion correction and patch CTF correction were performed in cryoSPARC.

5846923

Template picking

The published structure of the P. aeruginosa Cas1 homodimer (PDB:3GOD) was used as starting models for the two Cas1 homodimers in this complex. The Colabfold-predicted models for the P. aeruginosa IHF heterodimer, and the P. aeruginosa Cas2/3 subunit were used as starting models. The conformation of the DNA sequences within the E. coli IHF-DNA co-crystal structure (PDB: 1IHF) was used as starting models for DNA segments within the IHFdistal and IHFproximal DNA bends. For all other double stranded DNA segments, B-form DNA was used as a starting model. Single-stranded DNA segments were built in de novo.

1 3.48 FSC 0.143 CUT-OFF cryoSPARC 366794 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 4 275750.0 cryoSPARC emd_29280_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 409.72803 409.72803 409.72803 90.0 90.0 90.0 X Y Z -0.28146487 0.5623969 0.00045229838 0.020226385 1.067 1.067 1.067 AUTHOR ::::EMDATABANK.org::::EMD-29280:::: emd_29280_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 409.72803 409.72803 409.72803 90.0 90.0 90.0 X Y Z -0.25734305 0.5383186 0.0004514241 0.020251572 1.067 1.067 1.067 AUTHOR ::::EMDATABANK.org::::EMD-29280::::