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- PDB-5l35: Cryo-EM structure of bacteriophage Sf6 at 2.9 Angstrom resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l35 | ||||||
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Title | Cryo-EM structure of bacteriophage Sf6 at 2.9 Angstrom resolution | ||||||
![]() | Gene 5 protein | ||||||
![]() | VIRUS / phage / Sf6 | ||||||
Function / homology | Major capsid protein Gp5 / P22 coat protein - gene protein 5 / Gene 5 protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||
![]() | Zhao, H. / Tang, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy. Authors: Haiyan Zhao / Kunpeng Li / Anna Y Lynn / Keith E Aron / Guimei Yu / Wen Jiang / Liang Tang / ![]() Abstract: The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand ...The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses. | ||||||
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 929 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8314MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
| x 60
2 |
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3 | ![]()
| x 5
4 | ![]()
| x 6
5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 45590.840 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-CL / | |
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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: Shigella phage Sf6 / Type: VIRUS / Entity ID: #1 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 19.5 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION | |||||||||||||||
Natural host | Organism: Shigella flexneri / Strain: M94 | |||||||||||||||
Virus shell | Name: virus capsid / Diameter: 650 nm / Triangulation number (T number): 7 | |||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: purified Sf6 phage | |||||||||||||||
Specimen support | Grid material: COPPER | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 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 |
Image recording | Electron dose: 9 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68000 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 46.6 / Protocol: AB INITIO MODEL / Space: RECIPROCAL Target criteria: Pseudo-crystallographic R factor and stereochemistry |