Animation of Phage T4

Tom Goddard
September 15, 2022

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

Quantitative description of a contractile macromolecular machine
Alec Fraser, Nikolai S Prokhorov, Fang Jiao, B Montgomery Pettitt, Simon Scheuring, Petr G Leiman
Sci Adv. 2021 Jun 11;7(24)

What to show

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.

Protein Data Bank models

Here are the models we use


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 described here.

ChimeraX commands

Here is an explanation of the ChimeraX commands phage.cxc that create the phage model and record the animation.

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Create the 28 layers of the sheath from the single ring.
    # Define the custom helixwave command.
    # Create full sheath
    helixwave #3 28 time 0
  7. 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
  8. 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
  9. 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