2024-11-13 REL RCSB RCSB RCSB 2020-02-21 2021-02-24 2021-02-24 2024-11-13 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R03 AI135767 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM098621 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM116942 United States Density-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with Typhoid Toxin Nguyen T Song J Typhoid Toxin, A2B5, Antibody, Fab, TOXIN Ahn C Yang YA Neupane DP Nguyen T Richards AF Sim JH Mantis NJ Song J Mechanisms of typhoid toxin neutralization by antibodies targeting glycan receptor binding and nuclease subunits. Iscience US 24 102454 102454 2021 34113815 doi:10.1016/j.isci.2021.102454 2589-0042 6vx4 FULLOVERLAP Complex of TyTx11 Fab with Typhoid toxin Complex of TyTx11 Fab with Typhoid toxin 0 1 2 3 4 5
Map of Fab segment of IgG antibody TyTx11 in complex with purified Typhoid toxin
 Typhoid toxin 1 2 4 5
S. Typhi A2B5 toxin wild type
Salmonella enterica subsp. enterica serovar Typhi str. CT18 TyTx11 Fab 1 1 3
Fab segment of IgG antibody TyTx11
Mus musculus Variable Domain of Kappa Chain of TyTx11 Antibody Mus musculus Hybridoma 0.011689934999999999 1 Mus musculus LEVO DIQMTQSSSYLSVSQGDRVTITCKASDHIDNWLAWYQQKPGNAPRLLISGATSLKTGLPSRFSGSGSGKDFSLSITNLQT EDVASYYCQQYWRTPYTFGGGTKLEI Pertussis like toxin subunit B Salmonella enterica subsp. enterica serovar Typhi str. CT18 0.012563041999999998 5 Escherichia coli BL21(DE3) LEVO EWTGDNTNAYYSDEVISELHVGQIDTSPYFCIKTVKANGSGTPVVACAVSKQSIWAPSFKELLDQARYFYSTGQSVRIHV QKNIWTYPLFVNTFSANALVGLSSCSATQCFGPK A0A286LNT9 Variable Domain of Heavy Chain of Antibody TyTx11 Mus musculus 0.020049723000000002 1 Mus musculus LEVO EVQLQQSGPVLVKPGPSVKISCKASGYSFIDYFMNWVMQSHGKSLEWIGRIDPYSGDTFYNQKFKGKATLTVDKSSTTAH MELRSLASEDSAVYYCAREVLNYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTW NSGSPWYISFLKLNKIF(UNK)RE(UNK) Pertussis toxin-like subunit ArtA Salmonella enterica subsp. enterica serovar Typhi str. CT18 0.025117145 1 Escherichia coli BL21(DE3) LEVO VDFVYRVDSTPPDVIFRDGFSLLGYNRNFQQFISGRSCSGGSSDSRYIATTSSVNQTYAIARAYYSRSTFKGNLYRYQIR ADNNFYSLLPSITYLETQGGHFNAYEKTMMRLQREYVSTLSILPENIQKAVALVYDSATGLVKDGVSTMNASYLGLSTTS NPGVIPFLPEPQTYTQQRIDAFGPLISSCFSIGSVCHSHRGQRADVYNMSFYDARPVIELILSK A0A3Z7CEY9 Cytolethal distending toxin subunit B Salmonella enterica subsp. enterica serovar Typhi str. CT18 0.028149776999999997 1 Escherichia coli BL21(DE3) LEVO NISDYKVMTWNLQGSSASTESKWNVNVRQLLSGTAGVDILMVQEAGAVPTSAVPTGRHIQPFGVGIPIDEYTWNLGTTSR QDIRYIYHSAIDVGARRVNLAIVSRQRADNVYVLRPTTVASRPVIGIGLGNDVFLTAHALASGGPDAAAIVRVTINFFRQ PQMRHLSWFLAGDFNRSPDRLENDLMTEHLERVVAVLAPTEPTQIGGGILDYGVIVDRAPYSQRVEALRNPQLASDHYPV AFLARSCLEHHHHHH A0A447PE99 3.1.-.- singleParticle particle 0.2 7.5 15.0 Tris tris(hydroxymethyl)aminomethane 150.0 NaCl sodium chloride ETHANE 100 277.15 FEI VITROBOT MARK IV
blot for 2.0 second before plunging.
Freshly prepared size-exclusion-chromatography purified complex of TyTx11 IgG and Typhoid toxin wild-type
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 1.5 63000.0 NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 54.7 1 4K6L C1 3.12 FSC 0.143 CUT-OFF RELION 3.1 61478 NOT APPLICABLE NOT APPLICABLE emd_21429.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 255.84 255.84 255.84 90.0 90.0 90.0 X Y Z -0.047669347 0.12601173 0.0000015912465 0.0033823168 1.23 1.23 1.23 0.025 AUTHOR Full map 4K6L PDB experimental model 6GFF K PDB experimental model 1F11 B 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_21429_msk_1.map emd_21429_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 255.84 255.84 255.84 90.0 90.0 90.0 X Y Z -0.14418998 0.26059425 0.00024400842 0.0050504436 1.23 1.23 1.23 AUTHOR RELION 3 Postprocess Map - Masked emd_21429_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 255.84 255.84 255.84 90.0 90.0 90.0 X Y Z -0.16591254 0.26059425 0.0000026152848 0.0076761963 1.23 1.23 1.23 AUTHOR RELION 3 Postprocess Map emd_21429_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 255.84 255.84 255.84 90.0 90.0 90.0 X Y Z -0.07116292 0.14061975 0.0000021858623 0.005074164 1.23 1.23 1.23 AUTHOR Half map 2 emd_21429_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 208 208 208 0 0 0 208 208 208 255.84 255.84 255.84 90.0 90.0 90.0 X Y Z -0.060805947 0.15636823 0.000003044707 0.004835767 1.23 1.23 1.23 AUTHOR Half map 1