Cryo-electron microscopy structure of the filamentous bacteriophage IKe

Proceedings of the National Academy of Sciences of the United States of America
Jingwei XuYe Xiang

Abstract

The filamentous bacteriophage IKe infects Escherichia coli cells bearing IncN pili. We report the cryo-electron microscopy structure of the micrometer-long IKe viral particle at a resolution of 3.4 Å. The major coat protein [protein 8 (p8)] consists of 47 residues that fold into a ∼68-Å-long helix. An atomic model of the coat protein was built. Five p8 helices in a horizontal layer form a pentamer, and symmetrically neighboring p8 layers form a right-handed helical cylinder having a rise per pentamer of 16.77 Å and a twist of 38.52°. The inner surface of the capsid cylinder is positively charged and has direct interactions with the encapsulated circular single-stranded DNA genome, which has an electron density consistent with an unusual left-handed helix structure. Similar to capsid structures of other filamentous viruses, strong capsid packing in the IKe particle is maintained by hydrophobic residues. Despite having a different length and large sequence differences from other filamentous phages, π-π interactions were found between Tyr9 of one p8 and Trp29 of a neighboring p8 in IKe that are similar to interactions observed in phage M13, suggesting that, despite sequence divergence, overall structural features are maintained.

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Citations

Jul 18, 2019·Nanomaterials·Iruthayapandi Selestin RajaDong-Wook Han
Feb 20, 2020·Proceedings of the National Academy of Sciences of the United States of America·Abul K TarafderTanmay A M Bharat
Feb 6, 2020·Nature Reviews. Microbiology·Moïra B DionSylvain Moineau
Nov 30, 2019·Progress in Nuclear Magnetic Resonance Spectroscopy·Amir Goldbourt
Mar 5, 2021·Bioconjugate Chemistry·Caitlin M CarmodySam R Nugen

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Methods Mentioned

BETA
X-ray
NMR
circular dichroism
circular
fluorescence

Software Mentioned

BLAST
Relion2

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