+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41632 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Asymmetric reconstruction of mature PP7 virions | ||||||||||||||||||||||||
Map data | The mature PP7 virion | ||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||
Keywords | ssRNA phage / PP7 / Pepevirus / VIRUS | ||||||||||||||||||||||||
Function / homology | Function and homology information virion attachment to host cell pilus / T=3 icosahedral viral capsid / virion component / regulation of translation / RNA binding / identical protein binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||||||||||||||
Authors | Thongchol J / Zhang J / Zeng L | ||||||||||||||||||||||||
Funding support | United States, 7 items
| ||||||||||||||||||||||||
Citation | Journal: Science / Year: 2024 Title: Removal of type IV pili by a small RNA virus. Authors: Jirapat Thongchol / Zihao Yu / Laith Harb / Yiruo Lin / Matthias Koch / Matthew Theodore / Utkarsh Narsaria / Joshua Shaevitz / Zemer Gitai / Yinghao Wu / Junjie Zhang / Lanying Zeng / Abstract: The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through ...The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_41632.map.gz | 332.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-41632-v30.xml emd-41632.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_41632.png | 30.8 KB | ||
Filedesc metadata | emd-41632.cif.gz | 4.2 KB | ||
Others | emd_41632_half_map_1.map.gz emd_41632_half_map_2.map.gz | 335.3 MB 335.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41632 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41632 | HTTPS FTP |
-Validation report
Summary document | emd_41632_validation.pdf.gz | 951.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_41632_full_validation.pdf.gz | 950.9 KB | Display | |
Data in XML | emd_41632_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_41632_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41632 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41632 | HTTPS FTP |
-Related structure data
Related structure data | 8tuxMC 8tumC 8tuwC 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_41632.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The mature PP7 virion | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half map 1
File | emd_41632_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_41632_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Type IV twitching pilus
Entire | Name: Type IV twitching pilus |
---|---|
Components |
|
-Supramolecule #1: Type IV twitching pilus
Supramolecule | Name: Type IV twitching pilus / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1 |
Molecular weight | Theoretical: 240 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 / Component - Concentration: 1.0 x / Component - Name: PBS Details: 137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4, pH 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 5085 / Average electron dose: 50.85 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 644601 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |