7VFH

Cryo-EM structure of Vaccinia virus scaffolding protein D13 trimer sextet

Summary for 7VFH

• Entry DOI: 10.2210/pdb7vfh/pdb
• EMDB information: 31954
• Descriptor: Scaffold protein D13 (1 entity in total)
• Functional Keywords: scaffold, capsid, double-jelly-roll, viral protein
• Biological source: Vaccinia virus (strain Western Reserve) (VACV, Vaccinia virus (strain WR))
• Total number of polymer chains: 18
• Total formula weight: 1076709.94

Authors

Wolf, M.,Hyun, J.,Matsunami, H.,Kim, T.G. (deposition date: 2021-09-13, release date: 2022-02-23, Last modification date: 2024-06-19)

Primary citation

Hyun, J.,Matsunami, H.,Kim, T.G.,Wolf, M.
Assembly mechanism of the pleomorphic immature poxvirus scaffold.
Nat Commun, 13:1704-1704, 2022

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.

PubMed: 35361762
DOI: 10.1038/s41467-022-29305-5

Experimental method

ELECTRON MICROSCOPY (3.9 Å)