Introduction to ChimeraX for cryoEM Atomic Structures

Tom Goddard
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 7STH.

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)

Topics

• How to look at cryoEM map contour surfaces.
• Working with atomic models.
• Using AlphaFold Database atomic models.
• Fitting atomic models in maps.
• Morphing between atomic models to view conformational changes.

1. Look at EMDB 25428, 3.5A resolution, 60 MB file size.
   Command: open 25428 from emdb
2. Adjust threshold with histogram slider or command
   volume #1 level .03
3. Adjust step size to show full resolution.
   volume #1 step 1
4. Use soft lighting from toolbar for shadows.
   light soft
5. Save image with toolbar snapshot button.
   save irmap.png
   

   Working with atomic models

6. Open atomic model that was built into map
   open 7sth
7. Undisplay map with Models panel or command
   hide #1 model
8. Color by chain with Molecule Display toolbar or
   color #2 bychain
9. Show surfaces with Molecule Display toolbar or
   surface #2
10. Select insulin chain D with link in log or
    select /D
11. Color insulin yellow with menu Actions / Color / yellow or
    color sel yellow
    

    Show map quality near atomic model

12. Look at map near one helix of insulin.
13. Clear selection with menu Select clear
    select clear
14. Hide surfaces with Molecule Display toolbar.
    hide #2 surface
15. Select one insulin helix with ctrl-click on ribbon followed by up arrow key
    select /D:8-19
16. Hide ribbon except for selected helix
    hide ~sel ribbon
17. Show map with Models panel
    show #1 model
18. Use menu Tools / Volume Data / Surface Zone near selected atoms
    volume zone #1 near sel range 3
19. Change map style to Mesh in Volume Viewer panel
    volume #1 style mesh
20. Show atoms of helix with menu Actions / Atoms / show
    show sel
21. Color nitrogens blue, oxygens red with Molecule Display toolbar color heteroatom
    color sel byhet
    

    Using AlphaFold Database atomic models

22. Use an AlphaFold model to start building an atomic model from the map.
23. Fetch AlphaFold prediction for UniProt INSR_MOUSE using menu Tools / Structure Prediction / AlphaFold.
    alphafold match INSR_MOUSE
    
24. AlphaFold per-residue confidence coloring: high blue, low red.
25. Show AlphaFold predicted aligned error (PAE) plot with AlphaFold panel Error Plot button.
    alphafold pae #3 uniprot INSR_MOUSE
    
26. Color PAE domains using button on PAE plot. AlphaFold is not confident of the packing of different colored domains.
    alphafold pae #3 colorDomains true
    
27. Blue, yellow and pink domains are extracellular and in map. Green is cytoplasmic kinase not in map.

    Fitting atomic models in maps

28. Fit blue AlphaFold domain in map.
29. Delete residues outside blue domains 28-336.
    delete #3:1-27,337-end
30. Redisplay full map as surface.
    volume unzone ; volume style surface
31. Move blue domain into map with Move Model mouse mode from Right Mouse toolbar.
    ui mousemode right "translate selected models"
32. Ctrl click blue ribbon to select it.
    select #3
33. Move blue domain into map with right mouse (on Mac Option key + trackpad drag). Hold Shift key to rotate.
34. Use Fit button on Map toolbar to optimize position in map.
    fitmap #3 in #1
35. 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

36. Above article describes 10 conformations of insulin receptor.
37. Open inactive form of receptor, PDB 7SL1.
    open 7sl1
38. Show 7sth atomic model and hide map and alphafold model.
    show #2 model ; hide #1,3 model ; show #2 ribbon
39. Color by chain using Molecule Display toolbar.
    color bychain
40. Select atom of 7sl1 and align it by hand with move model mouse mode.
    
41. Calculate morph using command
    morph #2,4 same true
42. Reset morph slider to start and press Record button (red circle) to record a movie.
    movie record ; coordset #5 ; wait 50 ; movie encode
    
43. Separation of intracellular kinases inactivates them.