The virion is a flexible filament (worm-like chain) about 6 nm in diameter and 900 nm long. Several thousand copies of a small (50 amino-acid residues) elongated alpha-helical major coat protein subunit (the product of gene 8, or p8) in an overlapping shingle-like array form a hollow cylinder enclosing the circular single-stranded DNA genome. Each p8 subunit has a collection of basic residues near the C-terminus of the elongated protein and acidic residues near the N-terminus; these two regions are separated by about 20 hydrophobic (non-polar) residues. The shingle-like arrangement places the acidic residues of p8 near the outside surface of the cylinder, where they cause the virus particle to be negatively-charged; non-polar regions near non-polar regions of neighbouring p8 subunits, where non-polar interactions contribute to a notable physical stability of the virus particle; and basic residues near the centre of the cylinder, where they interact with the negatively-charged DNA phosphates at the core of the virion. Longer (or shorter) DNA molecules can be packaged, since more (or fewer) p8 subunits can be added during assembly as required to protect the DNA, making the phage useful for genetic studies. (This effect should not be confused with polyphage, which can package several separate and distinct DNA molecules). About 5 copies each of four minor proteins cap the two ends of the virion.
The molecular structure of the virion capsid (the assembly of p8 subunit proteins) has been determined by X-ray fiber diffraction, and structural models have been deposited in the Protein Data Bank. In particular, the series of fd and Pf1 virion structures deposited in the PDB over decades illustrate the improvements in methods for fiber diffraction data collection and computational analysis. Structures of the p3 capsid protein and the p5 replication/assembly protein have also been determined from X-ray crystallography and deposited in the PDB.