2024-11-06 REL RCSB RCSB RCSB 2020-09-22 2021-09-01 2021-09-01 2024-11-06 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R03 AI135767 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 GM098621 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 GM116942 United States Structure of TyTx1 Fab in Complex with Typhoid Toxin Nguyen T Feathers JR Typhoid Toxin, A2B5, Antibody, Fab, TOXIN Nguyen T Richards AF Neupane DP Feathers JR Yang YA Sim JH Byun H Lee S Ahn C Van Slyke G Fromme JC Mantis NJ Song J The structural basis of Salmonella A 2 B 5 toxin neutralization by antibodies targeting the glycan-receptor binding subunits. Cell Rep US 36 109654 109654 2021 34496256 doi:10.1016/j.celrep.2021.109654 2211-1247 7k7h FULLOVERLAP Complex of TyTx1 Fab with Typhoid toxin Complex of TyTx1 Fab with Typhoid toxin 0 1 2 3 4
Fab fragment generated by proteolytic cleavage of IgG antibody in complex with purified Typhoid toxin
 Typhoid toxin 1 1 4
S. Typhi A2B5 toxin pltA-E133A cdtB-H160Q double mutant (catalytically inactivated toxin)
Salmonella enterica subsp. enterica serovar Typhi TyTx1 Fab 1 2 3
Fab fragment generated by proteolytic cleavage of IgG antibody TyTx1
Mus musculus Pertussis like toxin subunit B Salmonella enterica subsp. enterica serovar Typhi str. CT18 0.012563041999999998 5 Escherichia coli BL21(DE3) LEVO EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHV QKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK A0A286LNT9 Fab Light Chain Variable Domain Mus musculus 0.012679397 1 Mus musculus LEVO DIVMSQSPSSLAVSAGEKVNMSCKSSQSLFNSRTRKNHLAWYQQKPGQSPKLMIYWASTGECVVRDRFTGSGCGTDFTLT ISSVQDEDRAVYLCKQSHNRALTFGCGTKLEMKR Fab Heavy Chain Variable Domain Mus musculus 0.012802131 1 Mus musculus LEVO EIQSQQCGPELVKPGSSVKVSCKASGYAFTNYKALGSKQSHGKSLEWIGYIDPYNSDSSYNQQFKDKATLTVDKSSSTAY MYLNSLTSEDSAVYYCAGLELTGTLPYWGQGTLVTVSA Pertussis toxin-like subunit ArtA Salmonella enterica subsp. enterica serovar Typhi str. CT18 0.00166597 1 Escherichia coli BL21(DE3) LEVO FYDARPVIELILSK A0A4Z0MXD9 singleParticle particle 0.2 7.5 15.0 Tris tris(hydroxymethyl)aminomethane 150.0 NaCl sodium chloride Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE ETHANE 100 277.15 FEI VITROBOT MARK IV
blot for 2.5 second before plunging.
Freshly prepared size-exclusion-chromatography purified complex of TyTx1 Fab and Typhoid toxin catalytically inactivated toxin double mutant.
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 1.5 49000.0 NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 53.0 1 4K6L C1 3.0 FSC 0.143 CUT-OFF RELION 3 326766 NOT APPLICABLE NOT APPLICABLE emd_22699.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.0350301 0.058804728 -0.0000014970027 0.0014786812 0.83 0.83 0.83 0.0102 AUTHOR Full map 4RHR PDB experimental model 1MHH A PDB experimental model 4H20 H PDB experimental model
Initial local fitting was done using Chimera and then Coot was used for rebuilding Fab variable domains into correct sequences. Refinement was performed using Real Space Refine in PHENIX and was iterated with manual building in Coot.
 emd_22699_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.15436555 0.20179145 0.000098710094 0.0037769529 0.83 0.83 0.83 AUTHOR Post-processed Masked Map emd_22699_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.15436555 0.20179145 -0.0000013791441 0.0046091345 0.83 0.83 0.83 AUTHOR Post-processed map emd_22699_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.039535433 0.07009322 -0.00000062006063 0.0026416695 0.83 0.83 0.83 AUTHOR Half-map 2 emd_22699_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 249.0 249.0 249.0 90.0 90.0 90.0 X Y Z -0.04499274 0.06997618 -0.0000021382277 0.0026401 0.83 0.83 0.83 AUTHOR Half-map 1