9OUZ

Icosahedral D3 expanded capsid

Summary for 9OUZ

• Entry DOI: 10.2210/pdb9ouz/pdb
• EMDB information: 70800 70831 70832 70834 70878 70884
• Descriptor: Major capsid protein (1 entity in total)
• Functional Keywords: c5 symmetry, bacteriophage, capsid, hk97 fold, virus
• Biological source: Pseudomonas phage D3
• Total number of polymer chains: 9
• Total formula weight: 385847.33

Authors

Belford, A.K.,Huet, A.,Maurer, J.B.,Duda, R.L.,Conway, J.F. (deposition date: 2025-05-29, release date: 2026-03-11)

Primary citation

Belford, A.K.,Maurer, J.B.,Duda, R.L.,Huet, A.,Conway, J.F.
Structural insights into scaffold-guided assembly of the Pseudomonas phage D3 capsid.
Nat Commun, 16:11586-11586, 2025

PubMed Abstract: Tailed bacteriophages comprise the largest structural family of viruses with close relatives in archaea and the eukaryotic herpesviruses. The common assembly pathway produces an icosahedrally symmetric protein shell, called capsid, into which the double-stranded DNA genome is packaged. While capsid sizes and amino acid sequences vary considerably, the major capsid protein (MCP) folds are remarkably similar throughout the family. To investigate the mechanisms governing capsid size, we characterize the procapsid and mature capsid of phage D3, which expresses an icosahedral lattice with Triangulation number T = 9. We find that the MCP scaffold domain binds to the interior capsid surface, acting as a clamp to constrain subunit interactions. Following scaffold digestion, the MCP capsid domains form strong interactions that maintain capsid structure throughout maturation. The scaffold constraints appear critical for capsid size determination and provide important understanding of the factors governing capsid assembly in general and expands our understanding of these ecologically and biomedically important viruses.

PubMed: 41274907
DOI: 10.1038/s41467-025-66648-1

Experimental method

ELECTRON MICROSCOPY (3.5 Å)