8EJ5 | pdb_00008ej5

Tail tip structure of Staphylococcus phage Andhra


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structure and host specificity of Staphylococcus epidermidis bacteriophage Andhra.

Hawkins, N.C.Kizziah, J.L.Hatoum-Aslan, A.Dokland, T.

(2022) Sci Adv 8: eade0459-eade0459

  • DOI: https://doi.org/10.1126/sciadv.ade0459
  • Primary Citation Related Structures: 
    8EGR, 8EGS, 8EGT, 8EJ5

  • PubMed Abstract: 

    Staphylococcus epidermidis 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 S. epidermidis -infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of 11 capsid and tail proteins. The capsid is a T = 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.


  • Organizational Affiliation
    • Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Macromolecule Content 

  • Total Structure Weight: 83.6 kDa 
  • Atom Count: 5,818 
  • Modeled Residue Count: 727 
  • Deposited Residue Count: 743 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
gp10, tail tip lysin (spike)473Staphylococcus phage AndhraMutation(s): 0 
Gene Names: Andhra_10
UniProt
Find proteins for A0A1S6L1H0 (Staphylococcus phage Andhra)
Explore A0A1S6L1H0 
Go to UniProtKB:  A0A1S6L1H0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S6L1H0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
gp1, tail tip protein
B, C, D
90Staphylococcus phage AndhraMutation(s): 0 
UniProt
Find proteins for A0A1S6L1I2 (Staphylococcus phage Andhra)
Explore A0A1S6L1I2 
Go to UniProtKB:  A0A1S6L1I2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S6L1I2
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI156636

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection