ELECTRON CRYSTALLOGRAPHY: Its role in proteomics, Present and future

1. ELECTRON CRYSTALLOGRAPHY: Its role in proteomics, Present and future Kenneth H. Downing Lawrence Berkeley National Laboratory

2. Resolution of present microscopes -- ~1Å, but much worse for biology Fundamental problem in obtaining biological data by EM is radiation damage Exposure ~ 10 electron/Å2, Noise ~ 30% in 1-Å pixel Improve signal-to-noise ratio by averaging many equivalent images

3. Crystals provide a large number of equivalent images in a single shot -- all in same orientation, so easy to average Examples of structures solved by Electron crystallography: Results, limitations, prospects…

4. Tubulin: A cytoskeletal protein of eukaryotic cells that is essential for many functions

5. Dimer > protofilament > microtubule

6. Protofilaments in microtubules, Zn-sheets Microtubule Zn-sheet 25 nm >1000 nm

7. Electron diffraction from tubulin crystal 2.7 Å 3.5 Å

8. 2fo - fc map after refinement

9. Tubulin Structure & Topology

10. GDP H3 Taxol b M-loop GTP a Tubulin dimer

11. Tubulin - drug interactions Drugs that interfere with microtubule dynamics can stop cell division Taxol stabilizes microtubules -- as do several other drugs: epothilones sarcodictyin / eleutherobin discodermolide many Taxol (paclitaxel) analogues • These can be studied by diffraction methods

12. Density map with Taxol

13. Microtubule-stabilizing drugs

14. 3-D Electron diffraction data

15. Reciprocal Lattice Line Data

16. Lattice line data for Taxol, epothilone Taxol epothilone-A

17. Epothilone - Taxol density map

18. Taxol, Epothilone-A, Eleutherobin and Discodermolide bound to tubulin GTP-binding domain M-loop Intermediate domain

19. 3-D Reconstruction of Microtubule Microtubules imaged in 400-kV EM, Boxed into ~500 Å segments Segments aligned to reference constructed from crystal structure - corrected in- and out-of-plane tilts, variations in axial twist Used 89 MT images, ~1200 segments, ~200,000 monomers Result ~8 Å resolution

20. Dimer > protofilament > microtubule

21. Microtubule image, boxed into segments

22. Microtubule map at 8 Angstroms

23. Lateral interactions H6 H2-S3 loop M-loop H3 H1-S2 loop H10

24. Summary - Tubulin structure solved by electron crystallography Drug interactions studied with diffraction data Microtubule structure by cryo-EM shows tubulin-tubulin interactions

25. BACTERIORHODOPSIN: A light-driven proton pump in bacteria Integral membrane protein Structural paradigm for all rhodopsins, G-protein coupled receptors

26. First 3-D structure solved by electron crystallography (1990; resolution ~3.5 Å) Refined structure, high resolution images ~1995 Higher-resolution 3-D structures by EM, x-ray

27. BR in projection at 2.6 Å resolution (Grigorieff, Beckmann, Zemlin 1995)

28. Bacteriorhodopsin photocycle

29. Summary - Bacteriorhodopsin structure solved by electron crystallography Conformational changes studied by electron diffraction EM resolution extended to ~ 3 Å High resolution x-ray diffraction finally elucidated mechanism of proton pumping

30. How can EM compete with x-ray diffraction? • it shouldn’t compete! New instrumentation, along with continuing methods development -- The keys to better and faster structure solutions Role for EM is mainly structures not amenable to x-ray

31. Our latest Electron Microscope

32. Energy-loss Filtered Diffraction Patterns unfiltered filtered

33. Energy-loss Filtered Diffraction Patterns unfiltered filtered

34. Microtubule doublets are tubulin complexes stabilized by interactions with many MAPS Doublet image at ~10 Å should reveal novel tubulin-tubulin interactions as well as some tubulin MAP interactions

35. The role of electron microscopy in proteomics: Electron crystallography gives single molecule structure at “atomic” resolution Ligand interactions and small conformational change can also be studied by crystallographic approaches EM is particularly good at studying large complexes