5LWG

Israeli acute paralysis virus heated to 63 degree - full particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Cryo-electron Microscopy Study of the Genome Release of the Dicistrovirus Israeli Acute Bee Paralysis Virus.

Mullapudi, E.Fuzik, T.Pridal, A.Plevka, P.

(2017) J Virol 91

  • DOI: https://doi.org/10.1128/JVI.02060-16
  • Primary Citation of Related Structures:  
    5LWG, 5LWI

  • PubMed Abstract: 

    Viruses of the family Dicistroviridae can cause substantial economic damage by infecting agriculturally important insects. Israeli acute bee paralysis virus (IAPV) causes honeybee colony collapse disorder in the United States. High-resolution molecular details of the genome delivery mechanism of dicistroviruses are unknown. Here we present a cryo-electron microscopy analysis of IAPV virions induced to release their genomes in vitro We determined structures of full IAPV virions primed to release their genomes to a resolution of 3.3 Å and of empty capsids to a resolution of 3.9 Å. We show that IAPV does not form expanded A particles before genome release as in the case of related enteroviruses of the family Picornaviridae The structural changes observed in the empty IAPV particles include detachment of the VP4 minor capsid proteins from the inner face of the capsid and partial loss of the structure of the N-terminal arms of the VP2 capsid proteins. Unlike the case for many picornaviruses, the empty particles of IAPV are not expanded relative to the native virions and do not contain pores in their capsids that might serve as channels for genome release. Therefore, rearrangement of a unique region of the capsid is probably required for IAPV genome release.


  • Organizational Affiliation

    Structural Virology, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1208Israeli acute paralysis virusMutation(s): 0 
UniProt
Find proteins for G0Z733 (Israeli acute paralysis virus)
Explore G0Z733 
Go to UniProtKB:  G0Z733
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0Z733
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP3B [auth C]300Israeli acute paralysis virusMutation(s): 0 
UniProt
Find proteins for G0Z733 (Israeli acute paralysis virus)
Explore G0Z733 
Go to UniProtKB:  G0Z733
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0Z733
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP2C [auth B]247Israeli acute paralysis virusMutation(s): 0 
UniProt
Find proteins for B3TZL7 (Israeli acute paralysis virus)
Explore B3TZL7 
Go to UniProtKB:  B3TZL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3TZL7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VP457Israeli acute paralysis virusMutation(s): 0 
UniProt
Find proteins for R4MP31 (Israeli acute paralysis virus)
Explore R4MP31 
Go to UniProtKB:  R4MP31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4MP31
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.10.1
MODEL REFINEMENTREFMAC5.8.0155

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilCzech Republicn. 355855
European Molecular Biology OrganizationGermany#3041

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Data collection
  • Version 1.4: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-12-11
    Changes: Other