1. Volume 14, Issue 8, Pages 2017-2029 (March 2016)
Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor 
Huzhang Mao, Mitul Saha, Emilio Reyes-Aldrete, Michael B. Sherman, Michael Woodson, Rockney Atz, Shelley Grimes, Paul J. Jardine, Marc C. Morais 
Cell Reports 
Volume 14, Issue 8, Pages (March 2016)
DOI: /j.celrep
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2. Cell Reports 2016 14, 2017-2029DOI: (10.1016/j.celrep.2016.01.058)
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3. Figure 1 The Bacteriophage phi29 dsDNA Packaging Motor
(A) Cut-away side view of the bacteriophage phi29 dsDNA packaging motor as determined by cryoEM. Molecular envelopes of the connector, pRNA, and ATPase are shown in green, magenta, and blue, respectively.
(B) Model of the mechano-chemical cycle of the packaging motor as determined by single-molecule experiments (Chistol et al., 2012). The top and bottom halves of the panel show the chemical and mechanical transitions in the dwell phase and burst phases, respectively. Selected points of the mechano-chemical cycle that are specifically referred to in the text are marked by asterisks.
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4. Figure 2
X-Ray Crystal Structure of the N-Terminal ATPase Domain of gp16
(A) Two views of a ribbon diagram of gp16. β sheets and α helices on the conserved ASCE core are shown in green and orange, respectively, and are numbered in the right image of the panel. Additional strands and helices characteristic of the HerA/FtsK clade of the ASCE superfamily are shown in pink and blue, respectively, and a blue oval indicates the position of the C-terminal OB domain.
(B) Topology diagram of gp16; colors and symbols are the same as in (A).
(C) The proposed adenine binding motif is shown in blue, the Walker A motif is in magenta, and the Walker B motif is in red. The proposed phosphosensor, catalytic glutamate, and arginine finger are shown as stick figures colored green, red, and cyan, respectively. The substrate analog AMP-PNP is shown as a stick figure; atoms are colored by element except for carbon, which is colored yellow to facilitate viewing.
(D) Stereo diagram of active site residues in gp16; some backbone atoms have been removed to facilitate viewing. Magnesium and waters are shown as green and red spheres, respectively.
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5. Figure 3
CryoEM Reconstruction of Packaging Particles Stalled via the Addition of Substrate Analog γ-S-ATP
(A) Cut-away side view; density corresponding to the capsid, DNA, connector, pRNA, and ATPase is colored gray, red, yellow, magenta, and blue, respectively.
(B) Close-up cut-away side view of the motor with atomic resolution structures of the connector (yellow), pRNA (magenta), ATPase (blue), and DNA (red) fitted into their corresponding densities. The C terminus of the ASCE domain of gp16 is indicated and is shown as purple van der Waal spheres. AMP-PNP is shown as van der Waal spheres colored as in Figure 2, the putative DNA translocating loop is colored green, density for the C-terminal OB domain is labeled “CTD,” and two observed DNA contacts are indicated.
(C) End-on views of the fitted pRNA and N-terminal ATPase domain of gp16 (contact one) viewed from outside the phage looking in (left) and inside the phage looking out (right).
(D) End-on views of the fitted pRNA and the OB domain of gp16 (contact two) viewed from outside the phage looking in (left) and inside the phage looking out (right).
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6. Figure 4 Identification of the trans-acting Arginine Finger R146
(A) Ribbon diagram of gp16; mechanistically important residues, including R146, are labeled. The AMP-PNP substrate is shown as a stick figure, and the Mg2+ ion as a green sphere. The walker A and putative DNA translocating loops are colored magenta and green, respectively; the α helix connecting the DNA translocating loop to the arginine finger R146 is shown in orange.
(B) SDS-PAGE gels showing the DNA packaging activity of gp16 mutants targeting arginines near R146. Arginine residues that cluster near the putative arginine finger R146 were mutated to lysine and assayed for the ability to support DNA packaging. To assess packaging, the packaged DNA that was protected from DNase treatment was extracted from particles and analyzed by agarose gel electrophoresis. Lanes were rearranged, indicated by a space between lanes, to facilitate viewing.
(C) Complementation experiments demonstrating that R146 is a trans-acting arginine finger. ATPase activity was measured for proheads complexed with mixtures of the catalytically inactive D/E mutant and the arginine finger mutant R146A. When mixed together, complementation occurs since the D/E mutant can contribute its arginine finger in trans to an adjacent R146A subunit (n = 4; error bars, SD). In a 50% mixing ratio, perfect complementation between a D/E adjacent to an R146 subunit would be 25%. Observed complementation between the mutants was 13.7% ± 1.6%. Similar results are obtained with the R146K mutant.
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7. Figure 5 Ring Structure of the gp16 and DNA
(A) Cross-eyed stereo diagram of the ring structure of gp16 based on fitting the X-ray structure of the monomer into its corresponding cryoEM density in a 5-fold averaged reconstruction of particles stalled during packaging via the addition of γ-S-ATP. The viewing direction is from outside the phage looking toward the interior. The putative DNA translocating loop is shown in green, the arginine finger R146 is shown as cyan van der Waal spheres, and the substrate analog AMP-PNP and DNA as van der Waal spheres colored by element.
(B) Stereo diagram of a side view of the gp16 ring, colored as in (A); the capsid would be above the ring, and the back half of the ring has been left out to facilitate viewing.
Cell Reports  , DOI: ( /j.celrep )
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