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The Johnson Laboratory


We present here movies developed in our lab on various projects.

1 HK97: Transition of subunit F between Prohead II and Head II (movie made by Ilya Gertsman)
The movie is a linear interpolation between the Prohead II crystal structure coordinates and the previously solved Head II structure. The region of the spine helix that undergoes the greatest amount of bending (residues 195-216) is colored in yellow. The region that stays invariant, including the P-loop and surrounding residues in the β-strands, lies underneath the spine helix.
Related paper:  

      Size: 4.8 MB
2 HK97: Isolated view of hexon expansion (movie made by Ilya Gertsman)
The view is tangential to the capsid surface and follows the expansion of a hexon subunit from the Prohead II state through previously characterized expansion states (EI, Balloon/H-I, H-II). The movie shows linear interpolations between the distinct intermediate states. Coordinates from EI were obtained from a Cryo-EM reconstruction8, while coordinates for Balloon and Head II were obtained from previously published crystal structures. The movie focuses on subunits E (brown) and D (blue), which exhibit large differences in tertiary bending. The differences in rotational motions between subunits appears related to the positions of the subunits in Prohead II, with the more vertically positioned subunits undergoing larger rotations. Subunit D is shown to rotate less during the transition from Prohead II to EI, while subunit E undergoes considerably more rotation. The orientation of the subunits and their corresponding magnitude in tertiary distortion is believed to occur during assembly into capsomers and may be accentuated during the inter-capsomer associations in Prohead I assembly.
Related paper:  

      Size: 5.8 MB
3 HK97: Isolated helix transitions (movie made by Ilya Gertsman)
The movie depicts the same transition from Prohead II to Head II, except only the spine helix is shown. The side chains are also depicted which demonstrates the degree of twisting that accompanies the bending motion in the helix during the transition.
Related paper:  

      Size: 4.6 MB
4 HK97: Conformational Lock Facilitates Capsid Expansion (movie made by Gabe Lander)
This movie shows the cross-section of the HK97 capsid, just before the final crosslinks form. The refined B-factors are mapped onto Cα coordinates from the three capsid conformations: EI-IV from cryo-EM; pEI-IV; and Head II. The pentons (red) are blurred to show that they are dynamic relative to the relatively ordered hexons (blue). Pentons sample up to 14Å of translational space but perturb minimally the hexons, which flex slightly to accommodate the dynamic penton. There is no experimental evidence that pentons move in a symmetric fashion as portrayed by the movie. In fact, conformational "coupling" between pentons must be mediated by the surrounding hexons. Since the subunits located at the hexon-hexon interface barely move when EI-IV converts to Head II, it is unlikely that different pentons move cooperatively.
Related paper:  

      Size: 1.7 MB
5 HK97: Formation of the Final Crosslink (movie made by Gabe Lander)
This movie depicts the formation of the G-F crosslink from a fixed frame-of-reference. A penton subunit (green) bears K169 in the dynamic tip (unseen) of its E-loop, and forms a crosslink with hexon F-subunit (blue) bearing N356 (yellow sphere). This reaction is catalyzed by E363 (red sphere) that resides in Domain P of another penton subunit (teal). The E-loop (white) rotates around an axis near end of the β-strands (residues 158 and 172) while the rest of the penton subunit makes a radial, outward translation with respect to the particle center. These two motions, if simultaneous, prevent K169 from making a net translation. The entire F-subunit rotates to bring the N356 closer to the penton E-loop tip. The E-loop must be held (down) in a Head II conformation to enable the final crosslink (yellow balls) to form. It must be reiterated that these conformational changes occur sixty times per capsid, and that they are not necessarily synchronized.
Related paper:  

      Size: 1.9 MB
6 HK97: Hexon Conformational Change (movie made by Gabe Lander)
This movie follows one hexon during the course of the EI-IV to Head II transition, viewed tangential (A) and normal (B) to the capsid shell. Every hexon subunit undergoes a rigid-body rotation, but the two peripentonal subunits (A and F, colored light blue) make the largest rotations. These conformational changes accommodate the different penton positions and preserve the inter-capsomer interactions.
Related paper:  

      Size: 5.6 MB
7 HK97: EI-IV to Head II Conformational Change (movie made by Gabe Lander)
This movie follows a super-penton (one penton and five surrounding hexons) during the course of the EI-IV to Head II transition, viewed tangential (A) and normal (B) to the capsid shell. Hexon are green, pentons are blue, and penton E-loops are white. The EI-IV to Head II conformational change is effected mostly by penton subunits and peripentonal hexon subunits.
Related paper:  

      Size: 9.75 MB
8 HK97 Crosslink Topology (movie made by Gabe Lander)
This animation illustrates the crosslink topology of the EI-IV and Head II capsid states, viewed down the icosahedral 5-fold axis. Penton subunits are dark blue, the surrounding hexons are light blue, and the subunits are labeled with white letters. Pentons are formed by five G-subunits that surround the icosahedral 5-fold axis, and hexons are formed by subunits A, B, C, D, E, and F that surround a local 6-fold axis. A 5-circle is a closed-pentamer of crosslinked hexon A-subunits that surrounds a penton. A 6-circle is a closed-hexamer of crosslinked subunits (B, C, D, E, F, and G) that surrounds a hexon. The order of crosslink formation is not completely known, but the 5-circles must close before the 6-circles do because the GF crosslink (red) is the last to form. The twelve 5-circles and sixty 6-circles (72 total protein circles) interlock at quasi- and true-3-fold axes of the mature Head II structure. The resulting unitary structure, called molecular chainmail, is resistant to denaturants, high temperatures, and proteolysis.
Related paper:  

      Size: 4.7 MB
9 HK97 procapsid-capsid expansion - Full capsid view (movie made by Jinghua Tang)
HK97 is shown to expand from Prohead II to Head II from the outside. The pentons that are located at the vertices are colored green, and the hexons are colored red and blue to delineate the two halves separated by the distinctive "skew". The four states used to derive the intermediate time points are Prohead II, Expansion Intermediate I, Expansion Intermediate III, and Head II

      Size: 9.5 MB
10 HK97 procapsid-capsid expansion - Cross-sectional view (movie made by Jinghua Tang)
This movie shows a cross-section of HK97 to illustrate the progressive thinning of the capsid wall and doubling of internal volume as a result of expansion. The cutaway view emphasizes the motion of the penton subunits (green) located at the vertices during the transition from EI-III to Head II. An extrusion motion of the pentons characterizes the final maturation steps, and affects the order in which cross-links can occur, as is described for the cross-link movie. In the last frame, the semi-transparent Prohead II cross-section is displayed again, showing that the magnitude of the conformational change would allow a Head II particle to completely envelope its precursor.

      Size: 10 MB
11 HK97 expansion: Asymm. unit - top view (movie made by Jinghua Tang)
These two movies show the contortion like motion that an isolated icosahedral asymmetric unit undergoes during the capsid expansion process from views normal (**) and tangential (*hkside.asu*) to the capsid shell. The icosahedral 2-fold (oval), 3-fold (triangle) and 5-fold (pentagon) axes are displayed in the first and last sets of frames. The A domains are blue, P domains are red, N-arms are yellow, and E-loops are green.

      Size: 9.5 MB
12 HK97 expansion: Asymm. unit - side view (movie made by Jinghua Tang)

      Size: 9.8 MB
13 NωV VLPs: CryoEM map of the Capsid (movie made by Tsutomu Matsui)

      Size: 14 MB
14 NωV VLPs: Time resolved cryo-EM studies: Difference map analysis (movie made by Tsutomu Matsui)

      Size: 11.6 MB
15 NωV VLPs: Large conformational changes upon maturation (movie made by Tsutomu Matsui)
Nudaurelia capensis omega virus-like particles have been characterized as a 480-A procapsid and a 410-A capsid, both with T=4 quasisymmetry. Procapsids transition to capsids when pH is lowered from 7.6 to 5.0.

      Size: 14 MB
16 NωV VLPs: Conformation changes - Closeup view
A close-up view of the virus capsid organization as the maturation process continues

      Size: 15.3 MB
17 NωV VLPs: Conformation changes - Asymmetric unit-tangential view
The 4 independent subunits of the icosahedral asymmetric unit of the virus during the maturation process (viewing tangential to the virus surface)

      Size: 5.6 MB
18 NωV VLPs: Conformation changes - Asymmetric unit
Following the movements of the 4 independent subunits of the icosahedral asymmetric unit of the virus (from the surface of the virus)

      Size: 6.7 MB
19 NωV VLPs: Conformation changes illustrated with Ig domains
Large scale rearragements illustrated using only the Ig like domains of the virus

      Size: 10.6 MB
20 NωV VLPs: Conformation changes during maturation
The cross-sectional view of VLPs showing large rearrangements in quaternary and tertiary structure of the Virus Like Particles (VLPs) during the process of maturation.

      Size: 9.2 MB
21 CCMV: Native to Swollen state (movie made by Chunxu Qu)
This movie illustrates the large conformational changes the native state CCMV virus particles (coat proteins) undergo to form swollen particles when the bound metal ions are removed or the pH is raised.

      Size: 8 MB
22 FHV: dsRNA controls capsid architecture (movie made by Gabe Lander)
This movie shows how the ordered dsRNA found in Flock House Virus Structure controlls the capsid architecture

      Size: 5.5 MB