+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5215 | |||||||||
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Title | Anthrax toxin PA63 in complex with 1G3 | |||||||||
Map data | Anthrax toxin component PA63 in complex with neutralizing antibody 1G3 | |||||||||
Sample |
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Keywords | anthrax toxin protective antigen neutralizing antibody | |||||||||
Biological species | Bacillus anthracis (anthrax bacterium) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 33.0 Å | |||||||||
Authors | Radjainia M / Hyun J / Leysath CE / Leppla SH / Mitra AK | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2010 Title: Anthrax toxin-neutralizing antibody reconfigures the protective antigen heptamer into a supercomplex. Authors: Mazdak Radjainia / Jae-Kyung Hyun / Clinton E Leysath / Stephen H Leppla / Alok K Mitra / Abstract: The tripartite protein exotoxin secreted by Bacillus anthracis, a major contributor to its virulence and anthrax pathogenesis, consists of binary complexes of the protective antigen (PA) heptamer ...The tripartite protein exotoxin secreted by Bacillus anthracis, a major contributor to its virulence and anthrax pathogenesis, consists of binary complexes of the protective antigen (PA) heptamer (PA63h), produced by proteolytic cleavage of PA, together with either lethal factor or edema factor. The mouse monoclonal anti-PA antibody 1G3 was previously shown to be a potent antidote that shares F(C) domain dependency with the human monoclonal antibody MDX-1303 currently under clinical development. Here we demonstrate that 1G3 instigates severe perturbation of the PA63h structure and creates a PA supercomplex as visualized by electron microscopy. This phenotype, produced by the unconventional mode of antibody action, highlights the feasibility for optimization of vaccines based on analogous structural modification of PA63h as an additional strategy for future remedies against anthrax. | |||||||||
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_5215.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-5215-v30.xml emd-5215.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_5215_1.png | 89.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5215 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5215 | HTTPS FTP |
-Validation report
Summary document | emd_5215_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_5215_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_5215_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5215 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5215 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5215.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Anthrax toxin component PA63 in complex with neutralizing antibody 1G3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Anthrax toxin component PA63 in complex with 1G3
Entire | Name: Anthrax toxin component PA63 in complex with 1G3 |
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Components |
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-Supramolecule #1000: Anthrax toxin component PA63 in complex with 1G3
Supramolecule | Name: Anthrax toxin component PA63 in complex with 1G3 / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 1.1 MDa / Method: Size-exclusion chromatography |
-Macromolecule #1: toxin
Macromolecule | Name: toxin / type: protein_or_peptide / ID: 1 / Name.synonym: protective antigen / Recombinant expression: Yes |
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Source (natural) | Organism: Bacillus anthracis (anthrax bacterium) / synonym: bacillus anthracis |
Recombinant expression | Organism: Bacillus subtilis (bacteria) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 9 / Details: 150mM NaCl, 50mM CHES |
Staining | Type: NEGATIVE Details: Holey grids with samples negatively stained across holes with 1% uranyl acetate |
Grid | Details: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 97000 times magnification |
Date | Sep 1, 2008 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 13 µm / Number real images: 40 / Average electron dose: 10 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder: single-tilt / Specimen holder model: OTHER / Tilt angle max: 45 |
-Image processing
Details | The particles were manually selected. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP / Number images used: 3459 |
Final two d classification | Number classes: 20 |