Introduction to ChimeraX for cryoEM Atomic Structures
April 25, 2022
for Wah Chiu's Stanford cryoEM class
Introduction to using ChimeraX to analyze cryoEM maps and atomic models.
We will look at recent mouse insulin receptor structures published March 31, 2022,
map EMDB 25428
and atomic model PDB
Synergistic activation of the insulin receptor via two distinct sites
Jie Li, Junhee Park, John P. Mayer, Kristofor J. Webb, Emiko Uchikawa, Jiayi Wu, Shun Liu, Xuewu Zhang, Michael H. B. Stowell, Eunhee Choi & Xiao-chen Bai
Nature Structural & Molecular Biology volume 29, pages 357-368 (2022)
How to look at cryoEM map contour surfaces
Look at EMDB 25428, 3.5A resolution, 60 MB file size.
Command: open 25428 from emdb
- Adjust threshold with histogram slider or command
volume #1 level .03
- Adjust step size to show full resolution.
volume #1 step 1
- Use soft lighting from toolbar for shadows.
- Save image with toolbar snapshot button.
Working with atomic models
- Open atomic model that was built into map
- Undisplay map with Models panel or command
hide #1 model
- Color by chain with Molecule Display toolbar or
color #2 bychain
- Show surfaces with Molecule Display toolbar or
- Select insulin chain D with link in log or
- Color insulin yellow with menu Actions / Color / yellow or
color sel yellow
Show map quality near atomic model
- Look at map near one helix of insulin.
- Clear selection with menu Select clear
- Hide surfaces with Molecule Display toolbar.
hide #2 surface
- Select one insulin helix with ctrl-click on ribbon followed by up arrow key
- Hide ribbon except for selected helix
hide ~sel ribbon
- Show map with Models panel
show #1 model
- Use menu Tools / Volume Data / Surface Zone near selected atoms
volume zone #1 near sel range 3
- Change map style to Mesh in Volume Viewer panel
volume #1 style mesh
- Show atoms of helix with menu Actions / Atoms / show
- Color nitrogens blue, oxygens red with Molecule Display toolbar color heteroatom
color sel byhet
Using AlphaFold Database atomic models
- Use an AlphaFold model to start building an atomic model from the map.
- Fetch AlphaFold prediction for UniProt INSR_MOUSE using
menu Tools / Structure Prediction / AlphaFold.
alphafold match INSR_MOUSE
- AlphaFold per-residue confidence coloring: high blue, low red.
- Show AlphaFold predicted aligned error (PAE) plot with AlphaFold panel Error Plot button.
alphafold pae #3 uniprot INSR_MOUSE
- Color PAE domains using button on PAE plot.
AlphaFold is not confident of the packing of different colored domains.
alphafold pae #3 colorDomains true
- Blue, yellow and pink domains are extracellular and in map. Green is cytoplasmic kinase not in map.
Fitting atomic models in maps
- Fit blue AlphaFold domain in map.
- Delete residues outside blue domains 28-336.
- Redisplay full map as surface.
volume unzone ; volume style surface
- Move blue domain into map with Move Model mouse mode from Right Mouse toolbar.
ui mousemode right "translate selected models"
- Ctrl click blue ribbon to select it.
- Move blue domain into map with right mouse (on Mac Option key + trackpad drag). Hold Shift key to rotate.
- Use Fit button on Map toolbar to optimize position in map.
fitmap #3 in #1
- Show atoms as spheres to see fit better. Clear selection (ctrl-click background) then Molecule Display toolbar show atoms and sphere style.
select clear ; show #3 ; style #3 sphere
Morphing between atomic models to view conformational changes
- Above article describes 10 conformations of insulin receptor.
- Open inactive form of receptor, PDB
- Show 7sth atomic model and hide map and alphafold model.
show #2 model ; hide #1,3 model ; show #2 ribbon
- Color by chain using Molecule Display toolbar.
- Select atom of 7sl1 and align it by hand with move model mouse mode.
- Calculate morph using command
morph #2,4 same true
- Reset morph slider to start and press Record button (red circle) to record a movie.
movie record ; coordset #5 ; wait 50 ; movie encode
- Separation of intracellular kinases inactivates them.