Here we show how to make an animation
of the injection system of phage T4
using ChimeraX software.
The idea of a wave-like tail contaction comes from this article which
discusses a different phage T6SS
We piece together the virus capsid, needle, sheath and baseplate from different
electron microscopy models and show the sheath contraction which drives the needle
through the host bacterial cell (not shown) to inject the viral genome.
The main steps are to move the different virus pieces to the correct positions and
apply symmetry to generate the capsid, needle and sheath from asymmetric units.
We animate the sheath (striped blue and white) twisting starting at the tip
and progressing to the capsid based using some custom Python code
helixwave.py described
here.
ChimeraX commands
Here is an explanation of the ChimeraX commands phage.cxc that
create the phage model and record the animation.
Create one ring of the extended sheath and align at the origin
# Open extended sheath helix ring
open 6j0b
# Delete second copy of ring and needle proteins
del #1/G-L,a-l
# Move ring to origin 0,0,0
measure center #1
# Center of mass of 16476 atoms = (143.53, 143.53, 134.14)
move -143.53,-143.53,-134.14 atoms #1 coord #1
Create one ring of the contracted sheath and align it
# Open contracted sheath helix ring
open 6j0c
# Delete second copy of ring
del /a-f
# Rename chains so they match the order of 6j0b for morphing
changechain #2 A,B,C,D,E,F F,E,D,C,B,A
# Align contracted the extended helix ring
matchmaker #2/A,B,C,D,E,F to #1/A-F pair ss cutoff none
Morph the single sheath ring between extended and contracted shapes
# Morph helix ring extended to contracted state
morph #1,2 play false
# Color sheath ring gray and blue
color #3 lightgray
color #3/A,C,E cornflowerblue
Create the needle, applying helical symmetry to one ring.
# Open needle structure
open 6j0b
# Delete sheath rings and second copy of needle helix ring
del #4/A-L,g-l
# Color needle
color #4 salmon
# Align with sheath
move -143.53,-143.53,-134.14 atoms #4 coord #4
# Create 28 ring needle helix from single ring
sym #4 H,39.3,19.9,28
Make the capsid, applying icosahedral symmetry to the asymmetric unit.
# Open capsid asymmetric unit
open 5vf3
# Make full icosahedral shell
sym #5 assembly 1 newmodel false
# Position capsid at top of sheath and needle
move z -420 model #5 coord #5
Create the 28 layers of the sheath from the single ring.
# Define the custom helixwave command.
open helixwave.py
# Create full sheath
helixwave #3 28 time 0
Open and align the pre-attachment and post-attachment baseplate that the virus uses to attach to a bacterium.
# Open pre-attachment baseplate
open 5iv5
# Align to tip of sheath
matchmaker #7/BD,DG,FJ,IC,T,q to #6.28 pair ss cutoff none
# Open post-attachment baseplate
open 5iv7
# Align to post-attachment baseplate to pre-attachment baseplate
matchmaker #8/BD,DF,GA,O,e,u to #6.28 pair ss cutoff none
# Hide pre-attachment baseplate
hide #8 model
Set the window size, camera view, and lighting for a movie.
# Make window tall and narrow for movie recording
windowsize 400 1000
# Orient vertically
view orient
turn x 90 center #5
zoom 1.7
move y 900
# Use ambient lighting
light soft
# Make small crevices darker
light msDepth 0.003
Record an animation of sheath contraction. The pre-attachment baseplate fades to the post-attachment baseplate then the sheath contracts.
# Draw first frame
wait 1
# Animate and record movie
movie record
# Fade out pre-attachment baseplate model and fade in post-attachment baseplate
crossfade 60 ; hide #7 model ; show #8 model
wait 60
# Animate twisting collapse of sheath moving needle and capsid downward
helixwave #6 move #4,5 steps 300
wait 300
# Record movie file
movie encode phage.mp4 framerate 60 quality higher
