6V8I

Composite atomic model of the Staphylococcus aureus phage 80alpha baseplate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage.

Kizziah, J.L.Manning, K.A.Dearborn, A.D.Dokland, T.

(2020) PLoS Pathog 16: e1008314-e1008314

  • DOI: https://doi.org/10.1371/journal.ppat.1008314
  • Primary Citation of Related Structures:  
    6V8I

  • PubMed Abstract: 

    Staphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and resistance factors in S. aureus are encoded by mobile genetic elements, and transduction by bacteriophages represents the main mechanism for horizontal gene transfer. The baseplate is a specialized structure at the tip of bacteriophage tails that plays key roles in host recognition, cell wall penetration, and DNA ejection. We have used high-resolution cryo-electron microscopy to determine the structure of the S. aureus bacteriophage 80α baseplate at 3.75 Å resolution, allowing atomic models to be built for most of the major tail and baseplate proteins, including two tail fibers, the receptor binding protein, and part of the tape measure protein. Our structure provides a structural basis for understanding host recognition, cell wall penetration and DNA ejection in viruses infecting Gram-positive bacteria. Comparison to other phages demonstrates the modular design of baseplate proteins, and the adaptations to the host that take place during the evolution of staphylococci and other pathogens.


  • Organizational Affiliation

    Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Distal Tail Protein, gp58315Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFC4 (Staphylococcus phage 80alpha)
Explore A4ZFC4 
Go to UniProtKB:  A4ZFC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFC4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tail-Associated Lysin, gp59C [auth AE],
G [auth CE],
K [auth BE]
633Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFC5 (Staphylococcus phage 80alpha)
Explore A4ZFC5 
Go to UniProtKB:  A4ZFC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFC5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tape Measure Protein, gp57D [auth CF],
H [auth BF],
L [auth AF]
1,154Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFC2 (Staphylococcus phage 80alpha)
Explore A4ZFC2 
Go to UniProtKB:  A4ZFC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFC2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fiber Lower, gp62607Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFC8 (Staphylococcus phage 80alpha)
Explore A4ZFC8 
Go to UniProtKB:  A4ZFC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFC8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fiber Upper, gp68390Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFD4 (Staphylococcus phage 80alpha)
Explore A4ZFD4 
Go to UniProtKB:  A4ZFD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFD4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Major Tail Protein, gp53193Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFB9 (Staphylococcus phage 80alpha)
Explore A4ZFB9 
Go to UniProtKB:  A4ZFB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFB9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor Binding Protein, gp61636Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFC7 (Staphylococcus phage 80alpha)
Explore A4ZFC7 
Go to UniProtKB:  A4ZFC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFC7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0-beta-2
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI083255

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description