Poly-Gly-Ala aggregates (red) surrounded by proteasomes (green) within a neuron from Guo Q, Cell Feb 2018

Proteasomes ChimeraX Tutorial

Tom Goddard
BCBB Training Seminars
September 11, 2019

We will show ChimeraX visualization of electron tomography 3d maps of proteasomes in fibril aggregates found in cultured rat neurons and associated with amyotrophic lateral sclerosis and frontotemporal dementia. We also look at how to fit atomic models of proteasomes into the proteasome shapes found in the aggregates.

The biological system is described in the following article

In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.
Guo Q, Lehmer C, Martinez-Sánchez A, Rudack T, Beck F, Hartmann H, Perez-Berlanga M,
Frottin F, Hipp MS, Hartl FU, Edbauer D, Baumeister W, Fernandez-Busnadiego R.
Cell. 2018 Feb 8;172(4):696-705.e12. doi: 10.1016/j.cell.2017.12.030. Epub 2018 Feb 1.
    

Data sets we will look at: tomogram EMDB 4191, subtomogram averaged proteasome EMDB 3915, atomic model PDB 5MPC.

Tomogram visualization

open 4191 from emdb
Switch to plane style in Volume Viewer panel.
Adjust yellow curve nodes to control brightness.
Adjust Plane slider to look at different slices.
volume scale #1 factor -1
view orient

Details

  1. Tomogram EMDB 4191 is 240 Mbytes and can be slow to download (size 926 x 926 x 71 grid points, 32-bit float values).
  2. ChimeraX caches fetched data under folder ~/Download/ChimeraX
  3. Tomogram intensity are traditionally inverted, meaning low values correspond to higher density. The values represent how much of the electron beam passed through the sample and hit the detector.
  4. It is sometimes useful for visualization to make high values correspond to high density as done above.
  5. The "volume scale" command creates a copy of the map in memory. It does not modify the original map.

Marking proteasomes

Zoom in and look for white rings with holes.
These are proteasomes.
Use Markers toolbar, click Plane icon.
Right click (Cmd+click on Mac) to place markers on proteasomes.
vol box #2 center sel size 300
hide #2
save ~/Desktop/proteasome1.mrc model #4

Details

  1. I made the red rings in the image as a large letter "o" with the 2dlabel command (2dlabel text o color red size 300) and positioned them with the move label mouse mode.
  2. Save markers to an XML text file with command "save ~/Desktop/proteasomes.cmm model #3"
  3. Guo Q, Cell Feb 2018 identified proteasomes with custom MATLAB and TOM toolbox template matching algorithms.

Surfaces

volume = 7.4896e+05
area = 87962
size = 325.01 111.15 115.29
Switch to surface style in volume viewer.
vol #2 style surface level 900
Hide small connected surface blobs.
surf dust #2 size 200
Use Blob mouse mode from toolbar.
Click proteasome surfaces to measure size.
Log output.

Details

  1. Blob mouse mode draws a box aligned with the principle axes of inertia and reports lengths along those axes.
  2. Blob coloring is lost when surface level is changed.

Fitting atomic models

Guo Q, Cell Feb 2018 averaged proteasomes from tomogram with 4 different shapes. They fit atomic structures of proteasomes degrading substrate or not bound to substrate to infer the state of the proteasomes and concluded many proteasomes are stalled, unable to digest the Poly-Gly-Ala fibrils.

We will fit an atomic model of a proteasome degrading substrate into one of their subtomogram average proteasome maps at 13 Angstroms resolution.

close all
open 3913 from emdb
open 5mpc
hide #1
view
select #2
Use translate and rotate selected mouse modes
to move atomic model into map.
Optimize fit.
fit #2 in #1
Delete extra proteins.
del /a-n,X
transparency #1 30

Details

  1. Guo's proteasome maps are half-proteasomes. The proteasome is a cylinder made of two rings and a lid complex on either end. A half proteasome has one ring and a lid.
  2. The fitmap command does a rigid rotation and translation to optimize the position of an atomic model in a map.
  3. To rotate with mouse or trackpad about the axis perpendicular to the screen click near the edge of the graphics window and drag.