5KIP

Asymmetric unit for the coat proteins of phage Qbeta


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Asymmetric cryo-EM structure of the canonical Allolevivirus Q beta reveals a single maturation protein and the genomic ssRNA in situ.

Gorzelnik, K.V.Cui, Z.Reed, C.A.Jakana, J.Young, R.Zhang, J.

(2016) Proc.Natl.Acad.Sci.USA 113: 11519-11524

  • DOI: 10.1073/pnas.1609482113

  • PubMed Abstract: 
  • Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjug ...

    Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A 2 , binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A 2 and the gRNA. A 2 contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.


    Organizational Affiliation

    Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843; junjiez@tamu.edu.,National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.,Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coat protein
A, B, C
133Escherichia phage QbetaMutation(s): 0 
Find proteins for P03615 (Escherichia phage Qbeta)
Go to UniProtKB:  P03615
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesA-1863
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103832
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM27099

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Data collection, Database references
  • Version 1.3: 2018-07-18
    Type: Data collection, Experimental preparation