6VX4

Density-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with Typhoid Toxin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanisms of typhoid toxin neutralization by antibodies targeting glycan receptor binding and nuclease subunits.

Ahn, C.Yang, Y.A.Neupane, D.P.Nguyen, T.Richards, A.F.Sim, J.H.Mantis, N.J.Song, J.

(2021) iScience 24: 102454-102454

  • DOI: https://doi.org/10.1016/j.isci.2021.102454
  • Primary Citation of Related Structures:  
    6VX4

  • PubMed Abstract: 

    Nearly all clinical isolates of Salmonella Typhi, the cause of typhoid fever, are antibiotic resistant. All S. Typhi isolates secrete an A 2 B 5 exotoxin called typhoid toxin to benefit the pathogen during infection. Here, we demonstrate that antibiotic-resistant S. Typhi secretes typhoid toxin continuously during infection regardless of antibiotic treatment. We characterize typhoid toxin antibodies targeting glycan-receptor-binding PltB or nuclease CdtB, which neutralize typhoid toxin in vitro and in vivo , as demonstrated by using typhoid toxin secreted by antibiotic-resistant S. Typhi during human cell infection and lethal dose typhoid toxin challenge to mice. TyTx11 generated in this study neutralizes typhoid toxin effectively, comparable to TyTx4 that binds to all PltB subunits available per holotoxin. Cryoelectron microscopy explains that the binding of TyTx11 to CdtB makes this subunit inactive through CdtB catalytic-site conformational change. The identified toxin-neutralizing epitopes are conserved across all S. Typhi clinical isolates, offering critical insights into typhoid toxin-neutralizing strategies.


  • Organizational Affiliation

    Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Variable Domain of Kappa Chain of TyTx11 AntibodyA [auth K]106Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis like toxin subunit BB [auth C],
D [auth A],
E [auth B],
F [auth D],
G [auth E]
114Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q8Z6A3 (Salmonella typhi)
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UniProt GroupQ8Z6A3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Variable Domain of Heavy Chain of Antibody TyTx11C [auth H]181Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin-like subunit ArtAH [auth G]224Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q8Z6A4 (Salmonella typhi)
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UniProt GroupQ8Z6A4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytolethal distending toxin subunit BI [auth F]255Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
Gene Names: 
cdtBABO08_07050ACK79_04015ACS18_04320ADQ64_04510AF726_04075AG53_02460AH360_09375AH874_08650AHN91_05150AHS86_01310AHX56_04670AHY46_21185AIA22_01750AID13_25040ALX58_21685AU833_04405AU920_00110AXO05_06525BXD49_09845BXO48_02100C3O10_15300CIJ14_23185D4382_23675D4E01_03970D4E24_23275D4E82_03815D4X65_01210D4Y21_22955D4Y61_01580D5769_01120D5773_04415D5806_21735D5905_00655D5938_05180D5A94_07255D5B66_02920D5P52_03820D5W53_03345D5X56_14350D6J84_12220D6Q32_04050D6Q48_23450D6Q50_22750D6R14_01875D6S47_01810D6S52_04640D7M89_03925D7O59_01230D8Q95_07260D8R18_22625D8R28_03780D8R78_05465D8S31_11805D9P30_01530D9P43_07260D9Q66_22865DAX91_01380DJ817_22940DJ902_22850DK094_15420DK681_22625DK719_00065DKA33_22680DKS84_01205DKT00_12650DL111_03690DLB36_01945DLC21_01190DM347_00605DM358_02585DMA89_03440DML97_01185DMM24_06680DMU80_01195DMU94_00450DMV34_24005DN115_03160DN181_02750DN218_09840DN257_00960DNM18_03225DNP18_20975DNU33_00605DNU46_06990DNV11_08545DNV24_09060DNV84_01240DNZ24_19360DNZ91_01190DO736_07435DO994_18310DOA32_23160DOC12_13865DOC15_02915DOC34_02235DOG98_22220DOH12_03665DOQ73_02885DOR42_02915DOR52_05945DOW79_02275DOX21_23175DP728_08755DP748_00630DP792_04070DP807_22370DP838_14200DPC30_05570DPD01_22830DPD54_23140DPE66_01635DPE90_12380DPJ07_11775DPK35_02680DPO73_22765DPR96_19355DPS68_01210DPT88_22945DPZ91_06800DQ837_03030DQ973_22635DQ986_03355DQC14_23020DQC85_22655DQJ66_20360DQJ71_17745DQK72_01185DQR07_01185DQS17_02890DQS90_22855DQY62_02055DQZ13_01205DRA30_01205DRF26_01185DRK15_02285DRK71_19590DRK91_13535DRL63_05765DRM75_04210DRT15_23155DRU74_02985DRV60_04480DRX43_08215DRY73_10160DRZ18_10315DS251_02230DS368_09485DS470_09640DS570_05080DS689_07420DSA82_02305DSA99_17640DSF62_00555DSQ94_23515DTE82_23795DTF17_02235DTF39_05055DTG02_04520DTG24_03875DTG49_09625DTG90_25155DTH05_08145DTT89_00540DTU25_03425DTW06_03295DU078_23475DU168_00610DU852_01200DU949_19355DUA52_03235DUC30_24990DUE02_01595DUP59_10365DUQ37_03210DUQ73_01530DUR82_01195DUR89_07585DUU35_01075DUU43_23100DUU47_01595DUV63_05900DVF01_11150EBC34_19090EBC39_01055ECA57_07075ED432_03555EDL32_22855EGM22_03890EGM32_22635EHB26_00195EHD17_22415EHF16_02745EIW64_10595EIW71_22510EIW76_01180GX90_01205JF03_03615KO25_07020LB54_02820NCTC8272_01874QC88_03775R126_05570R133_02035RY52_03905YR14_00925ZG82_07355

EC: 3.1
UniProt
Find proteins for Q8Z6A7 (Salmonella typhi)
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UniProt GroupQ8Z6A7
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.16-3549

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR03 AI135767
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM098621
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM116942

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references