Journal: Proc Natl Acad Sci U S A / Year: 2014 Title: Cryo-EM near-atomic structure of a dsRNA fungal virus shows ancient structural motifs preserved in the dsRNA viral lineage. Authors: Daniel Luque / Josué Gómez-Blanco / Damiá Garriga / Axel F Brilot / José M González / Wendy M Havens / José L Carrascosa / Benes L Trus / Nuria Verdaguer / Said A Ghabrial / José R Castón / Abstract: Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of ...Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of viral classes or lineages that can be grouped by capsid protein (CP) folds. Here, we report that the CP structure of the fungal dsRNA Penicillium chrysogenum virus (PcV) shows the progenitor fold of the dsRNA virus lineage and suggests a relationship between lineages. Cryo-EM structure at near-atomic resolution showed that the 982-aa PcV CP is formed by a repeated α-helical core, indicative of gene duplication despite lack of sequence similarity between the two halves. Superimposition of secondary structure elements identified a single "hotspot" at which variation is introduced by insertion of peptide segments. Structural comparison of PcV and other distantly related dsRNA viruses detected preferential insertion sites at which the complexity of the conserved α-helical core, made up of ancestral structural motifs that have acted as a skeleton, might have increased, leading to evolution of the highly varied current structures. Analyses of structural motifs only apparent after systematic structural comparisons indicated that the hallmark fold preserved in the dsRNA virus lineage shares a long (spinal) α-helix tangential to the capsid surface with the head-tailed phage and herpesvirus viral lineage.
History
Deposition
Mar 8, 2013
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Header (metadata) release
Jul 3, 2013
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Map release
May 14, 2014
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Update
Jun 25, 2014
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Current status
Jun 25, 2014
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Shell ID: 1 / Name: CP / Diameter: 400 Å / T number (triangulation number): 1
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7.8 / Details: 50 mM Tris-HCl , 150 mM NaCl, 5 mM EDTA
Grid
Details: C flat CF 1/2 4C grids
Vitrification
Cryogen name: ETHANE / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK II Method: Samples were applied to grids, blotted 7 seconds, and plunged into liquid ethane.
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Electron microscopy
Microscope
FEI TECNAI F30
Date
Feb 23, 2012
Image recording
Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 650 / Average electron dose: 25 e/Å2 / Bits/pixel: 8
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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