+Open data
-Basic information
Entry | Database: PDB / ID: 8egr | ||||||
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Title | Upper tail structure of Staphylococcus phage Andhra | ||||||
Components |
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Keywords | VIRUS / phage tail / portal / receptor-binding protein | ||||||
Function / homology | Portal protein Gp10 superfamily / Autotransporter, pectate lyase C-like domain superfamily / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / SGNH_hydro domain-containing protein / Peptidase S74 domain-containing protein / Adhesin / Upper collar protein Function and homology information | ||||||
Biological species | Staphylococcus phage Andhra (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å | ||||||
Authors | Kizziah, J.L. / Hawkins, N.C. / Dokland, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure and host specificity of bacteriophage Andhra. Authors: N'Toia C Hawkins / James L Kizziah / Asma Hatoum-Aslan / Terje Dokland / Abstract: is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages ... is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages with compact genomes that are attractive candidates for therapeutic use. Here, we report the structure of the complete virion of -infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of 11 capsid and tail proteins. The capsid is a = 4 icosahedron containing a unique stabilizing capsid lining protein. The tail includes 12 trimers of a unique receptor binding protein (RBP), a lytic protein that also serves to anchor the RBPs to the tail stem, and a hexameric tail knob that acts as a gatekeeper for DNA ejection. Using structure prediction with AlphaFold, we identified the two proteins that comprise the tail tip heterooctamer. Our findings elucidate critical features for virion assembly, host recognition, and penetration. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8egr.cif.gz | 904 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8egr.ent.gz | 722 KB | Display | PDB format |
PDBx/mmJSON format | 8egr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8egr_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8egr_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8egr_validation.xml.gz | 153.3 KB | Display | |
Data in CIF | 8egr_validation.cif.gz | 231.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/8egr ftp://data.pdbj.org/pub/pdb/validation_reports/eg/8egr | HTTPS FTP |
-Related structure data
Related structure data | 28128MC 8egsC 8egtC 8ej5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Symmetry | Point symmetry: (Schoenflies symbol: C6 (6 fold cyclic)) |
-Components
#1: Protein | Mass: 67393.203 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage Andhra (virus) / Gene: Andhra_15 / Production host: Staphylococcus phage Andhra (virus) / References: UniProt: A0A1S6L1H3 #2: Protein | Mass: 39219.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage Andhra (virus) / Gene: Andhra_17 / Production host: Staphylococcus phage Andhra (virus) / References: UniProt: A0A1S6L1H9 #3: Protein | Mass: 33070.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage Andhra (virus) / Production host: Staphylococcus phage Andhra (virus) #4: Protein | Mass: 46951.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage Andhra (virus) / Gene: Andhra_06 / Production host: Staphylococcus phage Andhra (virus) / References: UniProt: A0A1S6L1H1 #5: Protein | Mass: 12303.066 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage Andhra (virus) / Gene: Andhra_20 / Production host: Staphylococcus phage Andhra (virus) / References: UniProt: A0A1S6L1H7 |
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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: Staphylococcus phage Andhra / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Staphylococcus phage Andhra (virus) |
Source (recombinant) | Organism: Staphylococcus epidermidis (bacteria) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Staphylococcus epidermidis |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 39 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_4290: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154849 / Symmetry type: POINT | ||||||||||||||||||||||||
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