5KIP

Asymmetric unit for the coat proteins of phage Qbeta

Summary for 5KIP

• Entry DOI: 10.2210/pdb5kip/pdb
• EMDB information: 8253 8254 8255
• Descriptor: Coat protein (1 entity in total)
• Functional Keywords: qbeta, ssrna, phage, virus
• Biological source: Enterobacteria phage Qbeta
• Total number of polymer chains: 3
• Total formula weight: 42804.21

Authors

Gorzelnik, K.V.,Cui, Z.,Zhang, J. (deposition date: 2016-06-16, release date: 2016-10-05, Last modification date: 2024-03-06)

Primary citation

Gorzelnik, K.V.,Cui, Z.,Reed, C.A.,Jakana, J.,Young, R.,Zhang, J.
Asymmetric cryo-EM structure of the canonical Allolevivirus Q beta reveals a single maturation protein and the genomic ssRNA in situ.
Proc.Natl.Acad.Sci.USA, 113:11519-11524, 2016

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 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, 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 and the gRNA. A 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.

PubMed: 27671640
DOI: 10.1073/pnas.1609482113

Experimental method

ELECTRON MICROSCOPY (3.7 Å)