7VFF

Cryo-EM structure of Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Assembly mechanism of the pleomorphic immature poxvirus scaffold.

Hyun, J.Matsunami, H.Kim, T.G.Wolf, M.

(2022) Nat Commun 13: 1704-1704

  • DOI: https://doi.org/10.1038/s41467-022-29305-5
  • Primary Citation of Related Structures:  
    7VFD, 7VFE, 7VFF, 7VFG, 7VFH

  • PubMed Abstract: 

    In Vaccinia virus (VACV), the prototype poxvirus, scaffold protein D13 forms a honeycomb-like lattice on the viral membrane that results in formation of the pleomorphic immature virion (IV). The structure of D13 is similar to those of major capsid proteins that readily form icosahedral capsids in nucleocytoplasmic large DNA viruses (NCLDVs). However, the detailed assembly mechanism of the nonicosahedral poxvirus scaffold has never been understood. Here we show the cryo-EM structures of the D13 trimer and scaffold intermediates produced in vitro. The structures reveal that the displacement of the short N-terminal α-helix is critical for initiation of D13 self-assembly. The continuous curvature of the IV is mediated by electrostatic interactions that induce torsion between trimers. The assembly mechanism explains the semiordered capsid-like arrangement of D13 that is distinct from icosahedral NCLDVs. Our structures explain how a single protein can self-assemble into different capsid morphologies and represent a local exception to the universal Caspar-Klug theory of quasi-equivalence.


  • Organizational Affiliation

    Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, 904-0495, Onna-son, Okinawa, Japan. jhyu002@pusan.ac.kr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Scaffold protein D13
A, B, C
531Vaccinia virus WRMutation(s): 0 
Gene Names: VACWR118D13L
UniProt
Find proteins for P68440 (Vaccinia virus (strain Western Reserve))
Explore P68440 
Go to UniProtKB:  P68440
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68440
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101076
Japan Society for the Promotion of Science (JSPS)JapanJP17K07318
Japan Society for the Promotion of Science (JSPS)Japan21K06039

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Refinement description