2024-06-12 REL RCSB RCSB RCSB 2022-03-14 2022-12-07 2022-12-07 2024-06-12 National Science Foundation (NSF, United States) MCB-1616105 United States Structure of RecT protein from Listeria innoccua phage A118 in complex with 83-mer ssDNA Bell CE Caldwell BJ DNA Recombination, DNA Annealing, DNA BINDING PROTEIN Caldwell BJ Norris AS Karbowski CF Wiegand AM Wysocki VH Bell CE Structure of a RecT/Red beta family recombinase in complex with a duplex intermediate of DNA annealing. Nat Commun UK 13 7855 7855 2022 36543802 doi:10.1038/s41467-022-35572-z 2041-1723 EMD-26434 other EM volume
Maps for structure of LiRecT protein with two 83-mer strands
 7ubb FULLOVERLAP RecT protein from Listeria innocua phage A118, complexed with and 83-mer ssDNA RecT protein from Listeria innocua phage A118, complexed with and 83-mer ssDNA 0 1
The protein was purified by Nickel affinity and anion exchange chromatography. The DNA was chemically synthesized and HPLC purified.
Listeria innocua Clip11262 0.602 RecT Listeria innocua Clip11262 ATCC BAA-680 / CLIP 11262 0.030939099999999997
The modeled complex consists of 8 subunits of the RecT protein, which form a helical filament on ssDNA. The ssDNA was not modeled due to the low resolution. Density for four additional subunits, two on either end of the filament, was present, but not clear enough to dock into.
8 Escherichia coli BL21 LEVO GSHMATNDELKNQLANKQNGGQVASAQSLDLKGLLEAPTMRKKFEKVLDKKAPQFLTSLLNLYNGDDYLQKTDPMTVVTS AMVAATLDLPIDKNLGYAWIVPYKGRAQFQLGYKGYIQLALRTGQYKSINVIEVREGELLKWNRLTEEIELDLDNNTSEK VVGYCGYFQLINGFEKTVYWTRKEIEAHKQKFSKSDFGWKKDYDAMAKKTVLRNMLSKWGILSIDMQTAVTEDEAEPRER KDVTDDESIPDIIDAPVTPSDTLEAGSVVQGSMI Q92FL9 singleParticle particle 0.7 6.0 20.0 KH2PO4 Potassium phosphate 10.0 MgCl2 Magnesium chloride 0.075 n-dodecyl-beta-maltoside
The LiRecT protein was mixed at 37C with one oligonucleotide, and placed on ice for 90 min. Then immediately prior to vitrification, 1 ul of 1.5 mM n-dodecyl-beta-maltoside (Anatrace) was added (0.5 CMC).
 Quantifoil R1.2/1.3 GOLD 300 GLOW DISCHARGE AIR
60 seconds at 20 mA using a Pelco easiGlow
 ETHANE 100 277 FEI VITROBOT MARK IV
1.5 second blot time. Ted Pella 595 filter paper..
This sample was monodisperse
 FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 50.0 3.5 1.0 81000.0 Cs corrector was used GIF Bioquantum 20
Gatan BioContinuum energy filter
 GATAN K3 BIOQUANTUM (6k x 4k) 6000 4000 1 1619 2.83 65.0
45 fractions, 22.80 e-/A2/s
 1 1000 C1 4.5 FSC 0.143 CUT-OFF cryoSPARC 2.15.0
The final resolution with a tight mask was 4.5 Angstrom
180965 NOT APPLICABLE NOT APPLICABLE emd_26437.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 251.72 251.72 251.72 90.0 90.0 90.0 Z Y X -1.0352142 1.412036 0.000000000000168 0.0256524 0.899 0.899 0.899 0.05 AUTHOR Density Modified Map from PHENIX RESOLVE procedure AB INITIO MODEL
Phenix Real Space Refinement was by rigid body refinement of the eight different subunits. Due to the limited resolution, the refinement was limited to rigid body only.
REAL emd_26437_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 251.72 251.72 251.72 90.0 90.0 90.0 X Y Z -0.63552904 0.7211734 0.0010058604 0.08882082 0.899 0.899 0.899 EMDB Unmasked half-map from cryoSPARC emd_26437_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 251.72 251.72 251.72 90.0 90.0 90.0 X Y Z -0.7335553 0.68190616 0.0009973858 0.088574454 0.899 0.899 0.899 EMDB Unmasked half-map from cryoSPARC