2024-06-12 REL RCSB RCSB RCSB 2022-03-03 2022-08-31 2022-08-31 2024-06-12 National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) 1ZIAES102906 United States National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) 1ZICES103326 United States National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) 1ZIAES101905 United States Structure of E. coli dGTPase bound to T7 bacteriophage protein Gp1.2 and dGTP Klemm BP Dillard LB Borgnia MJ Schaaper RM dGTPase, inhibitor, substrate, complex, HYDROLASE Klemm BP Singh D Smith CE Hsu AL Dillard LB Krahn JM London RE Mueller GA Borgnia MJ Schaaper RM Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase. Proc.Natl.Acad.Sci.USA US 119 e2123092119 e2123092119 2022 36067314 doi:10.1073/pnas.2123092119 1091-6490 0040 PNASA6 7u66 FULLOVERLAP dGTPase hexamer bound to six copies of Gp1.2 dGTPase hexamer bound to six copies of Gp1.2 0 1 2 Escherichia coli str. K-12 substr. MG1655 dGTP triphosphohydrolase 1 1 Escherichia coli str. K-12 substr. MG1655 Gene 1.2 protein 1 2 Escherichia phage T7 Deoxyguanosinetriphosphate triphosphohydrolase Escherichia coli str. K-12 substr. MG1655 K12 0.05947086299999999 6 Escherichia coli BL21(DE3) LEVO MAQIDFRKKINWHRRYRSPQGVKTEHEILRIFESDRGRIINSPAIRRLQQKTQVFPLERNAAVRTRLTHSMEVQQVGRYI AKEILSRLKELKLLEAYGLDELTGPFESIVEMSCLMHDIGNPPFGHFGEAAINDWFRQRLHPEDAESQPLTDDRCSVAAL RLRDGEEPLNELRRKIRQDLCHFEGNAQGIRLVHTLMRMNLTWAQVGGILKYTRPAWWRGETPETHHYLMKKPGYYLSEE AYIARLRKELNLALYSRFPLTWIMEAADDISYCVADLEDAVEKRIFTVEQLYHHLHEAWGQHEKGSLFSLVVENAWEKSR SNSLSRSTEDQFFMYLRVNTLNKLVPYAAQRFIDNLPAIFAGTFNHALLEDASECSDLLKLYKNVAVKHVFSHPDVERLE LQGYRVISGLLEIYRPLLSLSLSDFTELVEKERVKRFPIESRLFHKLSTRHRLAYVEAVSKLPSDSPEFPLWEYYYRCRL LQDYISGMTDLYAWDEYRRLMAVEQ P15723 3.1.5.1 Inhibitor of dGTPase Escherichia phage T7 0.010595868
The additional N-terminal sequence is retained after cleavage of the expression tag with TEV protease.
6 Escherichia coli BL21(DE3) LEVO GSFTMGRLYSGNLAAFKAATNKLFQLDLAVIYDDWYDAYTRKDCIRLRIEDRSGNLIDTSTFYHHDEDVLFNMCTDWLNH MYDQLKDWK P03780 MAGNESIUM ION 2.4305e-05 6 MG 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE 0.000507181 6 DGT singleParticle particle 8.0 25.0 tris(hydroxymethyl)aminomethane Tris 75.0 Na3C6H5O7 Sodium citrate 10.0 MgCl2 Magnesium chloride 1.0 2-mercaptoethanol beta-mercaptoethanol UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE ETHANE 95 290 LEICA EM GP
Frozen stocks were thawed and mixed to a final concentration of 1.25:1 Gp1.2 to dGTPase (monomer) along with 1 mM dGTP
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.0 2.0 45000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1 1206 8.4 54.0 1
1037 micrographs used after eliminating micrographs with a CTF fit > 4.5 angstroms.
496081
Laplacian-of-Gaussian auto-picking
 Initial model from the dGTPase-Gp1.2-GTP dataset
Low-pass filtered to ~60 angstroms
 100 D3 FOURIER SPACE 3.1 FSC 0.143 CUT-OFF RELION 113934 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD RELION 200 617.0 RELION emd_26361.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 216.224 216.224 216.224 90.0 90.0 90.0 X Y Z -0.03305063 1.8492329 0.005818418 0.054332744 0.932 0.932 0.932 0.199 AUTHOR DeepEMhancer post-processed map RIGID BODY FIT
The dGTPase-Gp1.2 cryo-EM model was fit into the EM map, then the dGTP built in using Coot.
REAL emd_26361_msk_1.map emd_26361_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 216.224 216.224 216.224 90.0 90.0 90.0 X Y Z -0.02321702 0.05951439 0.00048931263 0.0037814006 0.932 0.932 0.932 AUTHOR Full map from RELION refinement emd_26361_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 216.224 216.224 216.224 90.0 90.0 90.0 Z Y X -9.503609000000001 19.389220999999999 -0.000000000005777 1.0 0.932 0.932 0.932 AUTHOR PHENIX auto-sharpened map emd_26361_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 216.224 216.224 216.224 90.0 90.0 90.0 X Y Z -0.17097285 0.28444088 0.0009023105 0.012577793 0.932 0.932 0.932 AUTHOR RELION post-processed map emd_26361_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 216.224 216.224 216.224 90.0 90.0 90.0 X Y Z -0.026470764 0.06359448 0.0004918791 0.004141263 0.932 0.932 0.932 AUTHOR Half-map 1 emd_26361_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 216.224 216.224 216.224 90.0 90.0 90.0 X Y Z -0.024369469 0.06558068 0.00048673688 0.0041300985 0.932 0.932 0.932 AUTHOR Half-map 2