+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22699 | ||||||||||||
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Title | Structure of TyTx1 Fab in Complex with Typhoid Toxin | ||||||||||||
Map data | Full map | ||||||||||||
Sample |
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Function / homology | Function and homology information NAD+-protein poly-ADP-ribosyltransferase activity / : / extracellular region Similarity search - Function | ||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi (bacteria) / Mus musculus (house mouse) / Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||
Authors | Nguyen T / Feathers JR / Fromme JC / Song J | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Cell Rep / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22699.map.gz | 80.8 MB | EMDB map data format | |
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Header (meta data) | emd-22699-v30.xml emd-22699.xml | 27.2 KB 27.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22699_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_22699.png | 53.7 KB | ||
Others | emd_22699_additional_1.map.gz emd_22699_additional_2.map.gz emd_22699_half_map_1.map.gz emd_22699_half_map_2.map.gz | 96.4 MB 7.3 MB 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22699 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22699 | HTTPS FTP |
-Validation report
Summary document | emd_22699_validation.pdf.gz | 729.1 KB | Display | EMDB validaton report |
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Full document | emd_22699_full_validation.pdf.gz | 728.7 KB | Display | |
Data in XML | emd_22699_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_22699_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22699 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22699 | HTTPS FTP |
-Related structure data
Related structure data | 7k7hMC 7k7iC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22699.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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_22699_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_22699_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_22699_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_22699_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of TyTx1 Fab with Typhoid toxin
Entire | Name: Complex of TyTx1 Fab with Typhoid toxin |
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Components |
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-Supramolecule #1: Complex of TyTx1 Fab with Typhoid toxin
Supramolecule | Name: Complex of TyTx1 Fab with Typhoid toxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Fab fragment generated by proteolytic cleavage of IgG antibody in complex with purified Typhoid toxin |
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-Supramolecule #2: Typhoid toxin
Supramolecule | Name: Typhoid toxin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4 Details: S. Typhi A2B5 toxin pltA-E133A cdtB-H160Q double mutant (catalytically inactivated toxin) |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Supramolecule #3: TyTx1 Fab
Supramolecule | Name: TyTx1 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 Details: Fab fragment generated by proteolytic cleavage of IgG antibody TyTx1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Mus musculus (house mouse) / Recombinant cell: Hybridoma |
-Macromolecule #1: Pertussis like toxin subunit B
Macromolecule | Name: Pertussis like toxin subunit B / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) |
Molecular weight | Theoretical: 12.563042 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 12.679397 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: DIVMSQSPSS LAVSAGEKVN MSCKSSQSLF NSRTRKNHLA WYQQKPGQSP KLMIYWASTG ECVVRDRFTG SGCGTDFTLT ISSVQDEDR AVYLCKQSHN RALTFGCGTK LEMKR |
-Macromolecule #3: Fab Heavy Chain Variable Domain
Macromolecule | Name: Fab Heavy Chain Variable Domain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 12.802131 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: EIQSQQCGPE LVKPGSSVKV SCKASGYAFT NYKALGSKQS HGKSLEWIGY IDPYNSDSSY NQQFKDKATL TVDKSSSTAY MYLNSLTSE DSAVYYCAGL ELTGTLPYWG QGTLVTVSA |
-Macromolecule #4: Pertussis toxin-like subunit ArtA
Macromolecule | Name: Pertussis toxin-like subunit ArtA / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) |
Molecular weight | Theoretical: 1.66597 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: FYDARPVIEL ILSK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 IV / Details: blot for 2.5 second before plunging. | |||||||||
Details | Freshly prepared size-exclusion-chromatography purified complex of TyTx1 Fab and Typhoid toxin catalytically inactivated toxin double mutant. |
-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: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
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 |
+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-7k7h: |