Cryo-EM structure of HzTransib/intact TIR substrate DNA pre-reaction complex (PRC)

2024-03-20 REL RCSB RCSB RCSB 2019-07-09 2019-07-17 2019-10-09 2024-03-20 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 1R01AI137079 United States Cryo-EM structure of HzTransib/intact TIR substrate DNA pre-reaction complex (PRC) Liu C Schatz DG Yang Y RAG-like transposase, DDE family enzyme, Transib, Terminal inverted repeat., RECOMBINATION, recombination-dna complex Liu C Yang Y Schatz DG Structures of a RAG-like transposase during cut-and-paste transposition. Nature UK 575 540 544 2019 31723264 doi:10.1038/s41586-019-1753-7 1476-4687 0006 NATUAS EMD-20453 other EM volume EMD-20455 other EM volume 6pqr FULLOVERLAP Pre-reaction complex of HzTransib with intact TIR substrate DNA Pre-reaction complex of HzTransib with intact TIR substrate DNA 0 1 2 3 Helicoverpa zea DNA-mediated transposase Helicoverpa zea 0.056582733999999996 2 Spodoptera frugiperda LEVO KPAPSTIFSPEKALGLLLSLKLSKWQYITLRETTIREGSKEIYPSYYKVQKAKLQCYPPKAFVAVTDSSAKIALQALLDL TVNRIFETIRSPDAIQNKQLILISKWGFDGASNQSRYKQNIESGQGDSSIFMTSLVPLKLTADGDTVWVNPKPCSPMYCR PVQFSFVKETKDVVINEKTAMDDEIEALVPSKCQGHEISHKLMMTMIDGKICTYLSEAKSNAACYLCLAKPTEMSKLDVI ASKTISSGVYEFGLSTLHARINVMECLLHIAYRLDFKKWSARGEGHQELLHSRKKLIQDRFKDDLNLLIDIVKQGSGTTN DGNTARRFFEFPDKTAAITGLDEDLIRRFSVILQAITSGEIIDVPKFKEYARTTAEKYVELYDWYYMSSTVHKLLIHGGD IIAENAIVPIGSLSEEASEARNKDFRRFREHHSRKKSRQASNEDILNMLIISSDPLISFTRPKLDAHKRQTYFKETVELL QLQDQEAPTEFHHHHHH B0F0C5 DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*TP*CP*AP*CP*GP*GP*TP*GP*GP*AP*TP*CP*GP*AP*AP*AP*A)-3') Helicoverpa zea 0.007402806 2 (DC)(DT)(DA)(DG)(DA)(DT)(DC)(DT)(DC)(DA)(DC)(DG)(DG)(DT)(DG)(DG)(DA)(DT)(DC)(DG) (DA)(DA)(DA)(DA) DNA DNA (5'-D(P*TP*TP*TP*TP*CP*GP*AP*TP*CP*CP*AP*CP*CP*GP*TP*GP*AP*GP*AP*TP*CP*TP*AP*G)-3') Helicoverpa zea 0.0073357399999999994 2 (DT)(DT)(DT)(DT)(DC)(DG)(DA)(DT)(DC)(DC)(DA)(DC)(DC)(DG)(DT)(DG)(DA)(DG)(DA)(DT) (DC)(DT)(DA)(DG) DNA MAGNESIUM ION 2.4305e-05 2 MG ZINC ION 6.5409e-05 2 ZN POTASSIUM ION 3.9098e-05 2 K singleParticle particle 0.3 7.5 20.0 NH2C(CH2OH)3 Tris 50.0 KCl potassium chloride 10.0 MgCl2 magnesium chloride 1.0 C9H15O6P Tris(2-carboxyethyl)phosphine

Solutions were made fresh from concentrated and filtered to avoid microbial contamination.

Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE 10 ETHANE 100 296 FEI VITROBOT MARK IV

Blot for 3 seconds before plunging.

Recombinantly expressed HzTransib transposase was mixed with chemically synthesized TIR substrate DNA. The complex was further purified on size-exclusion chromatography column. The final complex was monodisperse.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.4000000000000001 2.4 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20

Preliminary grid screening was performed manually.

GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1-40 50.8

Images were collected in movie-mode at 5 frames per second.

Startup model was generated ab initio in RELION

1 C2 3.4 FSC 0.143 CUT-OFF RELION 3.0 32984 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 8 10336.0 RELION 3.0 emd_20452.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 268.8 268.8 268.8 90.0 90.0 90.0 X Y Z -0.09705365 0.1410371 -0.000039340095 0.0037756374 1.05 1.05 1.05 0.0226 AUTHOR ::::EMDATABANK.org::::EMD-20452:::: 6PQN A 21-501 PDB experimental model RIGID BODY FIT

Initial local fitting was done using UCSF Chimera, then manually adjusted and rebuilt in Coot. Final model was refined using Phenix real-space refinement.

Correlation coefficient REAL