6EH1

Sacbrood virus of honeybee - expansion state II

  • Classification: VIRUS
  • Organism(s): Sacbrood virus
  • Mutation(s): No 

  • Deposited: 2017-09-12 Released: 2018-07-18 
  • Deposition Author(s): Plevka, P., Prochazkova, M.
  • Funding Organization(s): European Research Council, European Molecular Biology Organization

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Virion structure and genome delivery mechanism of sacbrood honeybee virus.

Prochazkova, M.Fuzik, T.Skubnik, K.Moravcova, J.Ubiparip, Z.Pridal, A.Plevka, P.

(2018) Proc Natl Acad Sci U S A 115: 7759-7764

  • DOI: https://doi.org/10.1073/pnas.1722018115
  • Primary Citation of Related Structures:  
    5LSF, 5OYP, 6EGV, 6EGX, 6EH1, 6EIW

  • PubMed Abstract: 

    Infection by sacbrood virus (SBV) from the family Iflaviridae is lethal to honey bee larvae but only rarely causes the collapse of honey bee colonies. Despite the negative effect of SBV on honey bees, the structure of its particles and mechanism of its genome delivery are unknown. Here we present the crystal structure of SBV virion and show that it contains 60 copies of a minor capsid protein (MiCP) attached to the virion surface. No similar MiCPs have been previously reported in any of the related viruses from the order Picornavirales. The location of the MiCP coding sequence within the SBV genome indicates that the MiCP evolved from a C-terminal extension of a major capsid protein by the introduction of a cleavage site for a virus protease. The exposure of SBV to acidic pH, which the virus likely encounters during cell entry, induces the formation of pores at threefold and fivefold axes of the capsid that are 7 Å and 12 Å in diameter, respectively. This is in contrast to vertebrate picornaviruses, in which the pores along twofold icosahedral symmetry axes are currently considered the most likely sites for genome release. SBV virions lack VP4 subunits that facilitate the genome delivery of many related dicistroviruses and picornaviruses. MiCP subunits induce liposome disruption in vitro, indicating that they are functional analogs of VP4 subunits and enable the virus genome to escape across the endosome membrane into the cell cytoplasm.


  • Organizational Affiliation

    Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
structural protein VP1211Sacbrood virusMutation(s): 0 
UniProt
Find proteins for Q9WCE9 (Sacbrood virus)
Explore Q9WCE9 
Go to UniProtKB:  Q9WCE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WCE9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
structural protein VP2179Sacbrood virusMutation(s): 0 
UniProt
Find proteins for A0A223DN66 (Sacbrood virus)
Explore A0A223DN66 
Go to UniProtKB:  A0A223DN66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A223DN66
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
structural protein VP3225Sacbrood virusMutation(s): 0 
UniProt
Find proteins for A0A223DN66 (Sacbrood virus)
Explore A0A223DN66 
Go to UniProtKB:  A0A223DN66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A223DN66
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
minor capsid protein MiCP26Sacbrood virusMutation(s): 0 
UniProt
Find proteins for Q9IGK7 (Sacbrood virus)
Explore Q9IGK7 
Go to UniProtKB:  Q9IGK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IGK7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilCzech RepublicFP/2007-2013 (355855)
European Molecular Biology OrganizationCzech RepublicIG-3041

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Other