+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26563 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Stx2a and DARPin complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information symbiont-mediated modulation of host virulence / hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region Similarity search - Function | |||||||||
Biological species | Escherichia phage 933W (virus) / Synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Jiang M / Zhang J | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Bioengineering (Basel) / Year: 2022 Title: A Multi-Specific DARPin Potently Neutralizes Shiga Toxin 2 via Simultaneous Modulation of Both Toxin Subunits. Authors: Yu Zeng / Mengqiu Jiang / Sally Robinson / Zeyu Peng / Vikas Chonira / Rudo Simeon / Saul Tzipori / Junjie Zhang / Zhilei Chen / Abstract: Shiga toxin-producing (STEC) is a common cause of bloody diarrhea. The pathology of STEC infection derives from two exotoxins-Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2)-that are secreted by STEC ...Shiga toxin-producing (STEC) is a common cause of bloody diarrhea. The pathology of STEC infection derives from two exotoxins-Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2)-that are secreted by STEC in the gut, from where they are systemically absorbed, causing severe kidney damage leading to hemolytic uremic syndrome (HUS). Currently, there is no effective treatment for HUS, and only supportive care is recommended. We report the engineering of a panel of designed ankyrin repeat proteins (DARPin) with potent neutralization activity against Stx2a, the major subtype associated with HUS. The best dimeric DARPin, SD5, created via a combination of directed evolution and rational design, neutralizes Stx2a with a half maximal effective concentration (EC) of 0.61 nM The two monomeric DARPin constituents of SD5 exhibit complementary functions-SHT targets the enzymatic A subunit of Stx2a and inhibits the toxin's catalytic activity, while DARPin #3 binds the B subunit, based on the cryo-EM study, and induces a novel conformational change in the B subunit that distorts its five-fold symmetry and presumably interferes with toxin attachment to target cells. SD5 was fused to an albumin-binding DARPin, and the resulting trimeric DARPin DA1-SD5 efficiently protects mice in a toxin challenge model, pointing to a high potential of this DARPin as a therapeutic for STEC infection. Finally, the unprecedented toxin conformational change induced by DARPin #3 represents a novel mode of action for neutralizing Stx2 toxicity and reveals new targets for future drug development. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_26563.map.gz | 59.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-26563-v30.xml emd-26563.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_26563.png | 56 KB | ||
Others | emd_26563_half_map_1.map.gz emd_26563_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26563 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26563 | HTTPS FTP |
-Validation report
Summary document | emd_26563_validation.pdf.gz | 757.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_26563_full_validation.pdf.gz | 757 KB | Display | |
Data in XML | emd_26563_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_26563_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26563 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26563 | HTTPS FTP |
-Related structure data
Related structure data | 7ujjMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_26563.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_26563_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_26563_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Ternary complex of stx2 and DARPin
+Supramolecule #1: Ternary complex of stx2 and DARPin
+Supramolecule #2: Shiga-like toxin 2 subunit A
+Supramolecule #3: Shiga-like toxin 2 subunit B
+Supramolecule #4: DARPin
+Macromolecule #1: DARPin
+Macromolecule #2: Shiga-like toxin 2 subunit A
+Macromolecule #3: Shiga-like toxin 2 subunit B
+Macromolecule #4: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
+Macromolecule #5: FORMIC ACID
+Macromolecule #6: SODIUM ION
+Macromolecule #7: 1,2-ETHANEDIOL
+Macromolecule #8: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108744 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |