Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 108.95 kDa 
• Atom Count: 7515 
• Modelled Residue Count: 982 
• Deposited Residue Count: 982 
• Unique protein chains: 1

3J3I

Penicillium chrysogenum virus (PcV) capsid structure

• PDB DOI: 10.2210/pdb3J3I/pdb
• EM Map EMD-5600:EMDBEMDataResource

• Classification: VIRUS
• Organism(s): Penicillium chrysogenum virus (isolate Caston)
• Mutation(s): No 


• Deposited: 2013-03-08 Released: 2014-05-14 
• Deposition Author(s): Luque, D., Gomez-Blanco, J., Garriga, D., Brilot, A., Gonzalez, J.M., Havens, W.H., Carrascosa, J.L., Trus, B.L., Verdaguer, N., Grigorieff, N., Ghabrial, S.A., Caston, J.R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM near-atomic structure of a dsRNA fungal virus shows ancient structural motifs preserved in the dsRNA viral lineage.

Luque, D., Gomez-Blanco, J., Garriga, D., Brilot, A.F., Gonzalez, J.M., Havens, W.M., Carrascosa, J.L., Trus, B.L., Verdaguer, N., Ghabrial, S.A., Caston, J.R.

(2014) Proc Natl Acad Sci U S A 111: 7641-7646

• PubMed: 24821769 
• DOI: 10.1073/pnas.1404330111
• Primary Citation of Related Structures:  
  3J3I


• PubMed 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 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.

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Organizational Affiliation: 

Department of Structure of Macromolecules, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Cientificas, Campus Cantoblanco, 28049 Madrid, Spain; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	982	Penicillium chrysogenum virus (isolate Caston)	Mutation(s): 0  Gene Names: p2
UniProt
Find proteins for Q8JVC1 (Penicillium chrysogenum virus (isolate Caston/2003)) Explore Q8JVC1  Go to UniProtKB:  Q8JVC1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-08 
• Released Date: 2014-05-14 
Deposition Author(s): Luque, D., Gomez-Blanco, J., Garriga, D., Brilot, A., Gonzalez, J.M., Havens, W.H., Carrascosa, J.L., Trus, B.L., Verdaguer, N., Grigorieff, N., Ghabrial, S.A., Caston, J.R.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-06-25
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Data collection