8R5I

In situ structure of the Vaccinia virus (WR) A4/A10 palisade trimer in mature virions by flexible fitting into a cryoET map


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Palisade structure in intact vaccinia virions.

Hernandez-Gonzalez, M.Calcraft, T.Nans, A.Rosenthal, P.B.Way, M.

(2024) mBio 15: e0313423-e0313423

  • DOI: https://doi.org/10.1128/mbio.03134-23
  • Primary Citation of Related Structures:  
    8R5I

  • PubMed Abstract: 

    Vaccinia virus assembly in the cytoplasm of infected cells involves the formation of a biconcave viral core inside the maturing viral particle. The boundary of the core is defined by a pseudohexagonal palisade layer, composed of trimers projecting from an inner wall. To understand the assembly of this complex core architecture, we obtained a subnanometer structure of the palisade trimer by cryo-electron tomography and subtomogram averaging of purified intact virions. Using AlphaFold2 structure predictions, we determined that the palisade is formed from trimers of the proteolytically processed form of the viral protein A10. In addition, we found that each A10 protomer associates with an α-helix (residues 24-66) of A4. Cellular localization assays outside the context of infection demonstrate that the A4 N-terminus is necessary and sufficient to interact with A10. The interaction between A4 and A10 provides insights into how the palisade layer might become tightly associated with the viral membrane during virion maturation. Reconstruction of the palisade layer reveals that, despite local hexagonal ordering, the A10/A4 trimers are widely spaced, suggesting that additional components organize the lattice. This spacing would, however, allow the adoption of the characteristic biconcave shape of the viral core. Finally, we also found that the palisade incorporates multiple copies of a hexameric portal structure. We suggest that these portals are formed by E6, a viral protein that is essential for virion assembly and required to release viral mRNA from the core early in infection.IMPORTANCEPoxviruses such as variola virus (smallpox) and monkeypox cause diseases in humans. Other poxviruses, including vaccinia and modified vaccinia Ankara, are used as vaccine vectors. Given their importance, a greater structural understanding of poxvirus virions is needed. We now performed cryo-electron tomography of purified intact vaccinia virions to study the structure of the palisade, a protein lattice that defines the viral core boundary. We identified the main viral proteins that form the palisade and their interaction surfaces and provided new insights into the organization of the viral core.


  • Organizational Affiliation

    Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein A10
A, C, E
614Vaccinia virus WRMutation(s): 0 
Gene Names: OPG136VACWR129A10L
UniProt
Find proteins for P16715 (Vaccinia virus (strain Western Reserve))
Explore P16715 
Go to UniProtKB:  P16715
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16715
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein A4
B, D, F
281Vaccinia virus WRMutation(s): 0 
Gene Names: OPG130VACWR123A4L
UniProt
Find proteins for P29191 (Vaccinia virus (strain Western Reserve))
Explore P29191 
Go to UniProtKB:  P29191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29191
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Database references