Note to the Paper by Guasch et al. (2002) Detailed Architecture of a DNA Translocating Machine: The High-resolution Structure of the Bacteriophage ϕ29 Connector Particle

The recent paper by Guasch et al.¹ describing the structure of the ϕ29 bacteriophage head–tail connector at 2.1 Å resolution (PDB code 1h5w), makes reference to the original 3.2 Å resolution structure (PDB code 1fou) published by Simpson et al.² and used by Guasch et al. to solve the 1h5w structure by molecular replacement. The Guasch paper states that there are marked differences between the 1h5w and 1fou structures in the chain tracing and the side-chain positioning in the wide domain. As these and a number of other statements in the Guasch paper may have led to the impression that these differences are larger than they really are, we give here Tables summarizing the similarities and differences (Tables 1 and 2).

Table 1.

Statistical comparison of the ϕ29 connector wide domains in different structures

	RMS deviation		Maximum deviation
	Cα atoms	All atoms	Cα atoms	All atoms	Number of Cα atoms deviating more than 2 Å
1h5w versus 1fou	1.1	2.2	4.9	10.6	15
1h5w versus 1jnb	1.2	2.0	5.2	11.1	10
1h5w versus 1ijg	0.8	1.6	6.4	11.4	5

The wide domain is defined as residues 38–128 and 247–284. All distances are in Å and correspond to comparisons of the A monomers in all structures.

Table 2.

Superposition of the entire monomers in the four reported structures

	RMS deviation		Maximum deviation
	Cα atoms	All atoms	Cα atoms	All atoms	Number of Cα atoms deviating more than 2 Å
1h5w versus 1fou	1.1	1.8	4.9	10.6	20
1h5w versus 1jnb	1.1	1.8	5.1	11.3	19
1h5w versus 1ijg	0.9	1.3	7.0	11.6	9a
1ijg versus 1jnb	1.1	1.9	6.0	11.8	18
Chain A versus chain B in 1ijg	0.9	1.5	7.5	13.8	6
Chain A versus chain B in 1h5w	0.5	0.8	4.4	6.5	2

The number of the aligned C^α atoms is 251. All distances are in Å.

^aThe number of differences greater than 2 Å varies from 1 to 9 depending on which of the 12 monomers are being compared.

Another paper by Simpson et al.,³ which was accidentally omitted from the text of the Guasch et al. paper, reports two additional structures of the ϕ29 connector: at 3.2 Å resolution and at 2.9 Å resolution (PDB codes 1jnb and 1ijg, respectively). The 2.9 Å resolution structure shows no significant differences from the structure subsequently reported by Guasch et al. (Figure 1; Tables 1 and 2).

Figure 1.

Stereo diagram showing the superposition of the C^α back-bone of monomer A in the 2.1 Å resolution structure 1h5w (green) and the 2.9 Å resolution 1ijg structure (red).