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Yorodumi- EMDB-21429: Density-fitted Model Structure of Antibody Variable Domains of Ty... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21429 | ||||||||||||
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Title | Density-fitted Model Structure of Antibody Variable Domains of TyTx11 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 / Transferases; Glycosyltransferases; Pentosyltransferases / : / endonuclease activity / toxin activity / Hydrolases; Acting on ester bonds / hydrolase activity / extracellular region Similarity search - Function | ||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) / Mus musculus (house mouse) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | ||||||||||||
Authors | Nguyen T / Song J | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: iScience / Year: 2021 Title: Mechanisms of typhoid toxin neutralization by antibodies targeting glycan receptor binding and nuclease subunits. Authors: Changhwan Ahn / Yi-An Yang / Durga P Neupane / Tri Nguyen / Angelene F Richards / Ji Hyun Sim / Nicholas J Mantis / Jeongmin Song / Abstract: Nearly all clinical isolates of Typhi, the cause of typhoid fever, are antibiotic resistant. All Typhi isolates secrete an AB exotoxin called typhoid toxin to benefit the pathogen during infection. ...Nearly all clinical isolates of Typhi, the cause of typhoid fever, are antibiotic resistant. All Typhi isolates secrete an AB exotoxin called typhoid toxin to benefit the pathogen during infection. Here, we demonstrate that antibiotic-resistant 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 and , as demonstrated by using typhoid toxin secreted by antibiotic-resistant 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 Typhi clinical isolates, offering critical insights into typhoid toxin-neutralizing 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_21429.map.gz | 26.4 MB | EMDB map data format | |
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Header (meta data) | emd-21429-v30.xml emd-21429.xml | 28.4 KB 28.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21429_fsc.xml | 7.4 KB | Display | FSC data file |
Images | emd_21429.png | 54.1 KB | ||
Masks | emd_21429_msk_1.map | 34.3 MB | Mask map | |
Others | emd_21429_additional_1.map.gz emd_21429_additional_2.map.gz emd_21429_half_map_1.map.gz emd_21429_half_map_2.map.gz | 32.2 MB 2.5 MB 26.4 MB 26.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21429 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21429 | HTTPS FTP |
-Validation report
Summary document | emd_21429_validation.pdf.gz | 188.9 KB | Display | EMDB validaton report |
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Full document | emd_21429_full_validation.pdf.gz | 188.4 KB | Display | |
Data in XML | emd_21429_validation.xml.gz | 502 B | Display | |
Data in CIF | emd_21429_validation.cif.gz | 373 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21429 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21429 | HTTPS FTP |
-Related structure data
Related structure data | 6vx4MC 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_21429.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21429_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: RELION 3 Postprocess Map
File | emd_21429_additional_1.map | ||||||||||||
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Annotation | RELION 3 Postprocess Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RELION 3 Postprocess Map - Masked
File | emd_21429_additional_2.map | ||||||||||||
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Annotation | RELION 3 Postprocess Map - Masked | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_21429_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_21429_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 TyTx11 Fab with Typhoid toxin
Entire | Name: Complex of TyTx11 Fab with Typhoid toxin |
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Components |
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-Supramolecule #1: Complex of TyTx11 Fab with Typhoid toxin
Supramolecule | Name: Complex of TyTx11 Fab with Typhoid toxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Map of Fab segment of IgG antibody TyTx11 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: #2, #4-#5 / Details: S. Typhi A2B5 toxin wild type |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Supramolecule #3: TyTx11 Fab
Supramolecule | Name: TyTx11 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #3 / Details: Fab segment of IgG antibody TyTx11 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Mus musculus (house mouse) / Recombinant cell: Hybridoma |
-Macromolecule #1: Variable Domain of Kappa Chain of TyTx11 Antibody
Macromolecule | Name: Variable Domain of Kappa Chain of TyTx11 Antibody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) / Cell: Hybridoma |
Molecular weight | Theoretical: 11.689935 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: DIQMTQSSSY LSVSQGDRVT ITCKASDHID NWLAWYQQKP GNAPRLLISG ATSLKTGLPS RFSGSGSGKD FSLSITNLQT EDVASYYCQ QYWRTPYTFG GGTKLEI |
-Macromolecule #2: Pertussis like toxin subunit B
Macromolecule | Name: Pertussis like toxin subunit B / type: protein_or_peptide / ID: 2 / 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 #3: Variable Domain of Heavy Chain of Antibody TyTx11
Macromolecule | Name: Variable Domain of Heavy Chain of Antibody TyTx11 / 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: 20.049723 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: EVQLQQSGPV LVKPGPSVKI SCKASGYSFI DYFMNWVMQS HGKSLEWIGR IDPYSGDTFY NQKFKGKATL TVDKSSTTAH MELRSLASE DSAVYYCARE VLNYYAMDYW GQGTSVTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSPWYI SFLKLNKIF(UNK) RE(UNK) |
-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: 25.117145 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: VDFVYRVDST PPDVIFRDGF SLLGYNRNFQ QFISGRSCSG GSSDSRYIAT TSSVNQTYAI ARAYYSRSTF KGNLYRYQIR ADNNFYSLL PSITYLETQG GHFNAYEKTM MRLQREYVST LSILPENIQK AVALVYDSAT GLVKDGVSTM NASYLGLSTT S NPGVIPFL ...String: VDFVYRVDST PPDVIFRDGF SLLGYNRNFQ QFISGRSCSG GSSDSRYIAT TSSVNQTYAI ARAYYSRSTF KGNLYRYQIR ADNNFYSLL PSITYLETQG GHFNAYEKTM MRLQREYVST LSILPENIQK AVALVYDSAT GLVKDGVSTM NASYLGLSTT S NPGVIPFL PEPQTYTQQR IDAFGPLISS CFSIGSVCHS HRGQRADVYN MSFYDARPVI ELILSK |
-Macromolecule #5: Cytolethal distending toxin subunit B
Macromolecule | Name: Cytolethal distending toxin subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) |
Molecular weight | Theoretical: 28.149777 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: NISDYKVMTW NLQGSSASTE SKWNVNVRQL LSGTAGVDIL MVQEAGAVPT SAVPTGRHIQ PFGVGIPIDE YTWNLGTTSR QDIRYIYHS AIDVGARRVN LAIVSRQRAD NVYVLRPTTV ASRPVIGIGL GNDVFLTAHA LASGGPDAAA IVRVTINFFR Q PQMRHLSW ...String: NISDYKVMTW NLQGSSASTE SKWNVNVRQL LSGTAGVDIL MVQEAGAVPT SAVPTGRHIQ PFGVGIPIDE YTWNLGTTSR QDIRYIYHS AIDVGARRVN LAIVSRQRAD NVYVLRPTTV ASRPVIGIGL GNDVFLTAHA LASGGPDAAA IVRVTINFFR Q PQMRHLSW FLAGDFNRSP DRLENDLMTE HLERVVAVLA PTEPTQIGGG ILDYGVIVDR APYSQRVEAL RNPQLASDHY PV AFLARSC LEHHHHHH |
-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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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2.0 second before plunging. | |||||||||
Details | Freshly prepared size-exclusion-chromatography purified complex of TyTx11 IgG and Typhoid toxin wild-type |
-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: 54.7 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: 63000 |
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-6vx4: |