1 / 43

Integrating EM Maps with X-ray Data for Improved Structural Models in Protein Biology

This study explores the integration of electron microscopy (EM) maps and X-ray crystallography data to enhance structural biology analysis. We investigate how varying resolutions affect model fitting, focusing on similarities and weight adjustments for low- and high-resolution data. Utilizing the Groel-ATP7-Groes and GP6 protein examples, we demonstrate techniques to refine models through phase assignment and electron density averaging, aiming to find optimal atomic configurations and improve our understanding of protein structures.

ria-pickett
Télécharger la présentation

Integrating EM Maps with X-ray Data for Improved Structural Models in Protein Biology

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Fitting EM maps into X-ray Data Alexei VaginYork Structural Biology LaboratoryUniversity of York

  2. Can we find solution? Weight of low resolution grows Low high Model Similarity 0 .1 0.2 0.3 0.4 0.5 Very likely Weight of high resolution grows Low high Model size 0.5 0.4 0.3 0.2 0.1 Very unlikely EM model

  3. Information in X-ray and EMmust overlap Resmin X-ray s Resmax EM

  4. Example 1 Groel-ATP7-Groes Map: EMD-1180 Fitted atomic model: PDB 2c7c X-ray: PDB 1sx4 ( 40 - 3 A )

  5. EM map as model

  6. EM map (sfcheck) from grid

  7. EM map (sfcheck) 7A

  8. Information in X-ray and EMmust overlap Resmin X-ray (40A) s Resmax EM (7A)

  9. ∆Ph =⃒Phxray - Phem⃒ MR solution (EM model)∆Ph =⃒Phxray - Phmodel⃒MR solution (fitted atomic model) ∆Ph 90o 50o Res: 11.1 9.1 7.7 6.7 5.9 5.3 4.8 4.3 4.0 A

  10. Map ( Fobs Phem ) 6Å

  11. What we can do with these phases 1. Help to find HA positions in the derivative 2. Extend phases by averaging electron density 3. Try to fit some fragments ( helix )

  12. EM map (4A) Modified map Averaging and Solvent flattening

  13. Map (FobsPhem) 4Å Modified map

  14. ∆Ph =⃒Phxray - Phem⃒ MR solution (EM model)∆Ph =⃒Phxray - Phmodel⃒ MR solution (fitted atomic model)∆Ph =⃒Phxray - Phaver⃒MR solution (after DM) ∆Ph 90o 50o Res: 11.1 9.1 7.7 6.7 5.9 5.3 4.8 4.3 4.0 A

  15. Free atom model

  16. ∆Ph =⃒Phxray - Phem⃒ MR solution (EM model)∆Ph =⃒Phxray - Phmodel⃒ MR solution (fitted atomic model)∆Ph =⃒Phxray - Phmodel_ref⃒ MR solution (refined atomic model)∆Ph =⃒Phxray - Phfree⃒ MR solution (free atom model after DM) ∆Ph 90o 50o Res: 9.4 7.4 6.1 5.2 4.5 4.0 3.6 3.3 3.0 A

  17. Map (FobsPhem) 3Å Map (FobsPhfree) 3Å (Free atom model after DM)

  18. Map (FobsPhfree) 3Å (Free atom model after DM)

  19. Map (FobsPhfree) 3Å (Free atom model after DM)

  20. Example 2 X-ray structure of GP6 protein of phage SPP1 ( 3.4 A ) Fred Antson at al. University of York

  21. EM map as model

  22. EM map (sfcheck 1) from grid

  23. EM map (sfcheck 2) 8A

  24. Information in X-ray and EMmust overlap Resmin X-ray (40A) s Resmax EM (8A)

  25. ∆Ph =⃒Phxray - Phem⃒ MR solution (EM model) ∆Ph 90o 50o Res: 10.3 8.3 6.9 6.0 5.2 4.7 4.2 3.8 3.5 A

  26. Map ( Fobs Phem ) 7Å

  27. What we can do with these phases 1. Help to find HA positions in the derivative 2. Extend phases by averaging electron density 3. Try to fit some fragments ( helix )

  28. ∆ Ph =⃒Phxray - Phem⃒ MR solution (EM model)∆ Ph =⃒Phxray - Phaver⃒ MR solution (after DM) ∆Ph 90o 50o Res: 10.3 8.3 6.9 6.0 5.2 4.7 4.2 3.8 3.5 A

  29. Free atom modelmodel was used only to compute initial phases

  30. ∆ Ph =⃒Phxray - Phem⃒ MR solution (EM model)∆ Ph =⃒Phxray - Phaver⃒ MR solution (after DM)∆ Ph =⃒Phxray - Phfree⃒ MR solution (free atom model after DM) ∆Ph 90o 50o Res: 10.3 8.3 6.9 6.0 5.2 4.7 4.2 3.8 3.5 A

  31. Final map 3.5 A

  32. Final map 3.5 A

  33. Map ( Fobs Phem ) Final map

  34. What we can do with these phases 1. Help to find HA positions in the derivative 2. Extend phases by averaging electron density 3. Try to fit some fragments ( helix )

  35. Fitting 17 x 13 helixes into final map by SAPTF

  36. Final map 3.5 A and helixes

  37. X-ray model and helixes

  38. Model: helix_17x13.pdb 1.Refinement 2.Compute map for refined model 3.Combine final map and map from model Final map Combine map

  39. ∆ Ph =⃒Phxray - Phem⃒ MR solution (EM model)∆ Ph =⃒Phxray - Phaver⃒ MR solution (after DM)∆ Ph =⃒Phxray - Phfree⃒ MR solution (free atom model after DM)∆ Ph =⃒Phxray - Phcomb⃒ combine map ∆Ph 90o 50o Res: 10.3 8.3 6.9 6.0 5.2 4.7 4.2 3.8 3.5 A

  40. The end http://www.ysbl.york.ac.uk/~alexei/

  41. SOLUTION_CHECK:Are twosolutions identical?Alexei VaginYork Structural Biology LaboratoryUniversity of York

  42. It is trivial. Xtest [Torigin] [Tsymm_op] Ytest Xtarget Alignment, Fitting Orientation and position differences

  43. The end

More Related