8VDC

SaPI1 portal structure in mature capsids without DNA

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Dubowvirus dv80alpha
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-12-14 Released: 2024-01-10 
  • Deposition Author(s): Mukherjee, A., Kizziah, J.L., Dokland, T.
  • Funding Organization(s): National Institutes of Health/Office of the Director, National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation.

Mukherjee, A.Kizziah, J.L.Hawkins, N.C.Nasef, M.O.Parker, L.K.Dokland, T.

(2023) J Mol Biol 436: 168415-168415

  • DOI: https://doi.org/10.1016/j.jmb.2023.168415
  • Primary Citation of Related Structures:  
    8V8B, 8VD4, 8VD5, 8VD8, 8VDC, 8VDE

  • PubMed Abstract: 

    Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.


  • Organizational Affiliation

    Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein511Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFA8 (Staphylococcus phage 80alpha)
Explore A4ZFA8 
Go to UniProtKB:  A4ZFA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFA8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Connector110Dubowvirus dv80alphaMutation(s): 0 
UniProt
Find proteins for A4ZFB5 (Staphylococcus phage 80alpha)
Explore A4ZFB5 
Go to UniProtKB:  A4ZFB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZFB5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesOD024978
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA013148
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM116789
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI083255

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references