3J40

Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from Cryo-EM and Modeling


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling.

Baker, M.L.Hryc, C.F.Zhang, Q.Wu, W.Jakana, J.Haase-Pettingell, C.Afonine, P.V.Adams, P.D.King, J.A.Jiang, W.Chiu, W.

(2013) Proc.Natl.Acad.Sci.USA 110: 12301-12306

  • DOI: 10.1073/pnas.1309947110

  • PubMed Abstract: 
  • High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alt ...

    High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3-5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit-subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages.


    Organizational Affiliation

    National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
gp10
N, M, H, K, I, J, L
111Salmonella phage epsilon15Mutation(s): 0 
Find proteins for Q858G5 (Salmonella phage epsilon15)
Go to UniProtKB:  Q858G5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
gp7
A, F, B, G, D, C, E
335Salmonella phage epsilon15Mutation(s): 0 
Find proteins for Q858G8 (Salmonella phage epsilon15)
Go to UniProtKB:  Q858G8
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Other
  • Version 1.2: 2013-07-24
    Type: Database references
  • Version 1.3: 2013-08-07
    Type: Database references
  • Version 1.4: 2018-07-18
    Type: Data collection