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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22700 | ||||||||||||
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Title | Density of TyTx4 Fab in Complex with Typhoid Toxin | ||||||||||||
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Function / homology | Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Enterotoxin / extracellular region / Pertussis-like toxin subunit![]() | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | ||||||||||||
![]() | Nguyen T / Feathers JR / Fromme JC / Song J | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The structural basis of Salmonella AB toxin neutralization by antibodies targeting the glycan-receptor binding subunits. Authors: Tri Nguyen / Angelene F Richards / Durga P Neupane / J Ryan Feathers / Yi-An Yang / Ji Hyun Sim / Haewon Byun / Sohyoung Lee / Changhwan Ahn / Greta Van Slyke / J Christopher Fromme / ...Authors: Tri Nguyen / Angelene F Richards / Durga P Neupane / J Ryan Feathers / Yi-An Yang / Ji Hyun Sim / Haewon Byun / Sohyoung Lee / Changhwan Ahn / Greta Van Slyke / J Christopher Fromme / Nicholas J Mantis / Jeongmin Song / ![]() Abstract: Many bacterial pathogens secrete AB toxins comprising two functionally distinct yet complementary "A" and "B" subunits to benefit the pathogens during infection. The lectin-like pentameric B subunits ...Many bacterial pathogens secrete AB toxins comprising two functionally distinct yet complementary "A" and "B" subunits to benefit the pathogens during infection. The lectin-like pentameric B subunits recognize specific sets of host glycans to deliver the toxin into target host cells. Here, we offer the molecular mechanism by which neutralizing antibodies, which have the potential to bind to all glycan-receptor binding sites and thus completely inhibit toxin binding to host cells, are inhibited from exerting this action. Cryogenic electron microscopy (cryo-EM)-based analyses indicate that the skewed positioning of the toxin A subunit(s) toward one side of the toxin B pentamer inhibited neutralizing antibody binding to the laterally located epitopes, rendering some glycan-receptor binding sites that remained available for the toxin binding and endocytosis process, which is strikingly different from the counterpart antibodies recognizing the far side-located epitopes. These results highlight additional features of the toxin-antibody interactions and offer important insights into anti-toxin strategies. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 191.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.1 KB 26.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 51.2 KB | ||
Others | ![]() ![]() ![]() ![]() | 227 MB 13.2 MB 193.9 MB 193.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 698.3 KB | Display | ![]() |
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Full document | ![]() | 697.9 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k7iMC ![]() 7k7hC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Full-map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Post-processed Map
File | emd_22700_additional_1.map | ||||||||||||
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Annotation | Post-processed Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Post-processed Masked Map
File | emd_22700_additional_2.map | ||||||||||||
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Annotation | Post-processed Masked Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_22700_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_22700_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of TyTx4 Fab with Typhoid Toxin Catalytic Inactivated Mutant
Entire | Name: Complex of TyTx4 Fab with Typhoid Toxin Catalytic Inactivated Mutant |
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Components |
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-Supramolecule #1: Complex of TyTx4 Fab with Typhoid Toxin Catalytic Inactivated Mutant
Supramolecule | Name: Complex of TyTx4 Fab with Typhoid Toxin Catalytic Inactivated Mutant type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Map of Fab fragment of proteolytically cleaved IgG antibody TyTx4 in complex with purified Typhoid toxin PltA E133A and CdtB H160Q double mutant |
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-Supramolecule #2: Typhoid Toxin Catalytically Inactivated Mutant
Supramolecule | Name: Typhoid Toxin Catalytically Inactivated Mutant / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: S. Typhi A2B5 toxin PltA E133A & CdtB H160Q double mutant |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: TyTx4 Fab
Supramolecule | Name: TyTx4 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 Details: Fab fragment generated by proteolytic cleavage of IgG antibody TyTx4 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Putative pertussis-like toxin subunit
Macromolecule | Name: Putative pertussis-like toxin subunit / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.563042 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: EWTGDNTNAY YSDEVISELH VGQIDTSPYF CIKTVKANGS GTPVVACAVS KQSIWAPSFK ELLDQARYFY STGQSVRIHV QKNIWTYPL FVNTFSANAL VGLSSCSATQ CFGPK |
-Macromolecule #2: Fab Light Chain Variable Domain
Macromolecule | Name: Fab Light Chain Variable Domain / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.753811 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DILLTQSPSI LSVSPGERVS FSCRASQSIG TSIHWYQQKP NGSPRLLIQY ASQSISGIPS RFSGSGSGTD FTLTINSVES EDIADYYCQ HTNGWPYTFG WGDHAGNKP |
-Macromolecule #3: Fab Heavy Chain Variable Domain
Macromolecule | Name: Fab Heavy Chain Variable Domain / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.15971 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VKLVESGGGL VKPGGSLKLS CAASGFAFST YDMSWVRQTP EKRLEWVATI SGGGSYTYYP DIVKGRFTIS RDNARNTLYL QMSSLRSED TALYFCVRQY YGSSNYGMDY WGQGTSVTVS |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK I / Details: blot for 2.0 second before plunging. | |||||||||
Details | Freshly prepared size-exclusion-chromatography purified complex between Fab fragment of TyTx4 and Typhoid toxin wild-type |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 49000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Details | 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. | ||||||||
Output model | ![]() PDB-7k7i: |