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Open data
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Basic information
Entry | Database: PDB / ID: 9k3n | ||||||||||||||||||||||||
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Title | The structure of Salmonella phage PJNS002 | ||||||||||||||||||||||||
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![]() | VIRUS / structual proteins | ||||||||||||||||||||||||
Function / homology | DNA![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å | ||||||||||||||||||||||||
![]() | Hu, W.L. / Chen, Y.B. / Wei, Y.M. / Gao, Y. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for Salmonella infection by two Microviridae phages. Authors: Wanlong Hu / Zhengjie Liu / Yuming Wei / Qucheng Bian / Weiqi Lan / Chongzheng Fan / Jiaoyang Song / Qianqian Sun / Xiaojie Zhang / Yuqing Liu / Yan Gao / Yibao Chen / ![]() Abstract: The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage ...The global resurgence of multidrug-resistant Salmonella species, responsible for millions of annual infections, underscores the urgent need for alternative antimicrobial strategies, such as phage therapy. Microviridae phages offer a promising model for studying phage-host interactions with their unique structural and infection mechanisms. Here, we identify two Microviridae phages, PJNS001 and PJNS002, with different host receptor dependencies, and determine their cryo-EM structures at 2.68 Å and 2.59 Å resolution, respectively. These icosahedral capsids with T = 1 symmetry exhibit a unique vertex reinforcement mechanism, stabilizing the viral assembly. The specific pentameric adaptations, coupled with DNA binding protein engagements and thermodynamic constraints, collectively preclude the formation of hybrid virions. Structural analysis and in situ visualization reveal spike protein features and host-attachment intermediates, informing host specificity. Together, these findings advance our understanding of Microviridae infection mechanisms and provide a structural framework for rational phage design against antibiotic-resistant pathogens. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 848 KB | Display | |
Data in CIF | ![]() | 1.3 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 62023MC ![]() 9k3mC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 48418.332 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 18864.549 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein/peptide | Mass: 2929.386 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) ![]() #4: DNA chain | Mass: 1521.077 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) ![]() #5: DNA chain | Mass: 1207.870 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) ![]() Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Microviridae / Type: VIRUS / Details: T=1 icosahedral virus / Entity ID: #1-#3 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 4.31 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION | |||||||||||||||||||||||||
Natural host | Organism: Salmonella | |||||||||||||||||||||||||
Virus shell | Diameter: 290 nm / Triangulation number (T number): 1 | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: pH 7.2~7.6 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.25 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3827 |
Image scans | Width: 5760 / Height: 4092 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 528658 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86486 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 18.15 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |