Volume 18, Issue 2, Pages 149-159 (April 2005) Conservation of the Capsid Structure in Tailed dsDNA Bacteriophages: the Pseudoatomic Structure of ϕ29  Marc C. Morais, Kyung H. Choi, Jaya S. Koti, Paul R. Chipman, Dwight L. Anderson, Michael G. Rossmann  Molecular Cell  Volume 18, Issue 2, Pages 149-159 (April 2005) DOI: 10.1016/j.molcel.2005.03.013 Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 1 Cryo-EM Image Reconstructions of Fibered and Fiberless Isometric ϕ29 Particles (A) Three-dimensional image reconstruction of the fiberless isometric particle viewed down an icosahedral 2-fold axis contoured at 3σ. Approximate molecular envelopes for three monomers in the T = 3 icosahedral asymmetric unit of the particle are shown in blue, red, and green and are labeled “a,” “b,” and “c,” respectively. The pentameric and hexameric capsomers to which they belong are shown in gray. The BIG2 domains of each monomer are shaded more darkly. (B) Three-dimensional image reconstruction of the fibered isometric particle viewed down an icosahedral 2-fold axis contoured at 1σ. (C) Fibered minus fiberless particle difference map contoured at 1σ. Figure 1A is contoured at 3σ to facilitate visualization of molecular boundaries, whereas Figures 1B and 1C are contoured at 1σ to facilitate recognition of the more flexible fiber density. The icosahedral asymmetric unit of each map is shown as a black triangle, with 5-, 3-, and 2-fold axes shown as pentamers, triangles, and ovals, respectively. Molecular Cell 2005 18, 149-159DOI: (10.1016/j.molcel.2005.03.013) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 2 Identification of Secondary Structural Elements and Fold Recognition in the Isometric Particle (A) Stereodiagram showing the fit of the three major helices (shown in green) in the cryo-EM density, as found by the program Helixhunter. (B) Stereodiagram showing the fit of the HK97 capsid protein (red) into the cryo-EM density of a gp8 monomer. The three helices found by Helixhunter are shown in green. The three major helices of HK97 are labeled α3, α5, and α6 in accordance with the HK97 nomenclature. (C) Fit of the pseudoatomic model of gp8. The HK97-like domain is shown in red and the BIG2-like domain in magenta. The N and C termini of each domain are labeled. Molecular Cell 2005 18, 149-159DOI: (10.1016/j.molcel.2005.03.013) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 3 Pseudoatomic Structure of the ϕ29 Isometric Particle (A) Stereodiagram showing the fit of the atomic model of gp8 pentamers (blue) to the cryo-EM density of fiberless particles. The three major helices of HK97 are labeled α3, α5, and α6. (B) Stereodiagram showing the fit of the pseudoatomic model of gp8 hexamers to the cryo-EM density of fiberless particles. The two monomers related by icosahedral 3-fold symmetry are shown in red and green, respectively. The three major helices of HK97 are labeled α3, α5, and α6. (C) Stereodiagram of the pseudoatomic structure of the ϕ29 isometric particle. Individual monomers are colored as described in (A) and (B). (D) Central section showing the fit of the pseudoatomic structure of the ϕ29 isometric particle to cryo-EM density. Molecular Cell 2005 18, 149-159DOI: (10.1016/j.molcel.2005.03.013) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 4 Stereodiagram of the Pseudoatomic Structure of the ϕ29 Fibered Isometric Particle and the Interaction between the BIG2 Domain and the Particle Fibers The HK97-like domains corresponding to subunits a, b, and c are colored blue, red, and green, respectively, and all BIG2 domains are shown in magenta. The atomic structure of a trimeric coiled coil (T4 fibritin, PDB accession code 1AVY, shown in yellow) has been fitted into the cryo-EM fiber density. Molecular Cell 2005 18, 149-159DOI: (10.1016/j.molcel.2005.03.013) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 5 Cryo-EM Image Reconstruction of the ϕ29 Prohead (A) Three-dimensional image reconstruction of the fiberless prohead viewed perpendicular to the 5-fold axis of the particle. Four structurally distinct hexamers are colored yellow, red, green, and pink. (B) Triangulation net of a prolate ϕ29 particle, with the positions of hexamers and pentamers indicated. The specific hexamers indicated in (A) are colored accordingly. (C) The four structurally distinct hexamers viewed down their quasi-6-fold axes. The hexamers are colored as in (A). The BIG2 domain, which is rotated ∼180° from its expected position, is indicated by darker shading and an arrow showing the approximate rotation. Molecular Cell 2005 18, 149-159DOI: (10.1016/j.molcel.2005.03.013) Copyright © 2005 Elsevier Inc. Terms and Conditions

Figure 6 Pseudoatomic Structure of ϕ29 Proheads (A) Stereodiagram showing the fit of the pseudoatomic model of gp8 pentamers (blue) to cryo-EM density. (B) Stereodiagram showing the fit of the pseudoatomic model of gp8 hexamers to cryo-EM density. The two monomers related by local 3-fold symmetry are shown in red and green, respectively. (C) Stereodiagram of the pseudoatomic structure of ϕ29 proheads. Individual monomers are colored as described in (A) and (B). (D) Central section showing fit of pseudoatomic structure of ϕ29 proheads to cryo-EM density; the 5-fold axis of the phage is in the plane of the page. (E) Stereodiagram showing the fit of the connector protein (yellow) and the pRNA (magenta) to the cryo-EM density. Density interpreted as corresponding to the pRNA is colored green, and density interpreted as corresponding to the connector or gp8 is colored gray. Molecular Cell 2005 18, 149-159DOI: (10.1016/j.molcel.2005.03.013) Copyright © 2005 Elsevier Inc. Terms and Conditions