+Open data
-Basic information
Entry | Database: PDB / ID: 7yfw | ||||||
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Title | Cyanophage Pam3 fiber | ||||||
Components | Pam3 fiber proreins | ||||||
Keywords | VIRAL PROTEIN / fiber / VIRUS | ||||||
Biological species | uncultured cyanophage (environmental samples) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å | ||||||
Authors | Yang, F. / Jiang, Y.L. / Zhou, C.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Fine structure and assembly pattern of a minimal myophage Pam3. Authors: Feng Yang / Yong-Liang Jiang / Jun-Tao Zhang / Jie Zhu / Kang Du / Rong-Cheng Yu / Zi-Lu Wei / Wen-Wen Kong / Ning Cui / Wei-Fang Li / Yuxing Chen / Qiong Li / Cong-Zhao Zhou / Abstract: The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail ...The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yfw.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yfw.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 7yfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yfw_validation.pdf.gz | 1000.2 KB | Display | wwPDB validaton report |
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Full document | 7yfw_full_validation.pdf.gz | 999.7 KB | Display | |
Data in XML | 7yfw_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 7yfw_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/7yfw ftp://data.pdbj.org/pub/pdb/validation_reports/yf/7yfw | HTTPS FTP |
-Related structure data
Related structure data | 33799MC 7yfzC 8hdrC 8hdsC 8hdtC 8hdwC M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 27323.789 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) uncultured cyanophage (environmental samples) |
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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 |
-Sample preparation
Component | Name: uncultured cyanophage / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: uncultured cyanophage (environmental samples) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Pseudanabaena mucicola |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 3.1 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING ONLY |
3D reconstruction | Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45155 / Symmetry type: POINT |