7CHK

Cryo-EM Structure of Apple Latent Spherical Virus (ALSV)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release.

Naitow, H.Hamaguchi, T.Maki-Yonekura, S.Isogai, M.Yoshikawa, N.Yonekura, K.

(2020) Commun Biol 3: 488-488

  • DOI: https://doi.org/10.1038/s42003-020-01217-4
  • Primary Citation of Related Structures:  
    7CHK

  • PubMed Abstract: 

    Picorna-like plant viruses are non-enveloped RNA spherical viruses of ~30 nm. Part of the survival of these viruses depends on their capsid being stable enough to harbour the viral genome and yet malleable enough to allow its release. However, molecular mechanisms remain obscure. Here, we report a structure of a picorna-like plant virus, apple latent spherical virus, at 2.87 Å resolution by single-particle cryo-electron microscopy (cryo-EM) with a cold-field emission beam. The cryo-EM map reveals a unique structure composed of three capsid proteins Vp25, Vp20, and Vp24. Strikingly Vp25 has a long N-terminal extension, which substantially stabilises the capsid frame of Vp25 and Vp20 subunits. Cryo-EM images also resolve RNA genome leaking from a pentameric protrusion of Vp24 subunits. The structures and observations suggest that genome release occurs through occasional opening of the Vp24 subunits, possibly suppressed to a low frequency by the rigid frame of the other subunits.


  • Organizational Affiliation

    Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP20 protein176Apple latent spherical virusMutation(s): 0 
UniProt
Find proteins for Q9JGP1 (Apple latent spherical virus)
Explore Q9JGP1 
Go to UniProtKB:  Q9JGP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JGP1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP24 protein192Apple latent spherical virusMutation(s): 0 
UniProt
Find proteins for Q9JGP1 (Apple latent spherical virus)
Explore Q9JGP1 
Go to UniProtKB:  Q9JGP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JGP1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP25 protein217Apple latent spherical virusMutation(s): 0 
UniProt
Find proteins for Q9JGP1 (Apple latent spherical virus)
Explore Q9JGP1 
Go to UniProtKB:  Q9JGP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JGP1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan16H04757
Japan Society for the Promotion of Science (JSPS)Japan24657111
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations