A table and a few great detergents.
All steps on the road to higher standards.

In our September, 2016 newsletter, we curated a list of recent membrane protein structures determined by single particle electron cryo-microscopy (cryo-EM), and which detergents were used in those experiments. In the year that has elapsed, we are continuing to witness a substantial growth in the number of protein structures determined by this method. 

At the time of our last update (9/2016), there were slightly over 650 unique (<95% sequence identity) cryo-EM structures deposited in the PDB. As of 8/2017, there are now close to 950 unique structures, an impressive growth! A similar trend is seen when looking at the subset of membrane proteins determined by cryo-EM, with a growth from 44 to 79 unique membrane protein structures over the same time period(1). Thus far, in 2017, we have seen exciting new membrane protein structures determined by Cryo-EM, including: the Nav1.4-ß1 complex(2), the GluA2-AMPA receptor in complex with intact TARP γ2(3), the Multidrug ABC Transporter ABCG2 (also known as breast cancer resistance protein)(4), the Human ether-à-go-go-related potassium channel (hERG)(5), the Triheteromeric NMDA receptor(6), and the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)(7). Once again, we have compiled a table of the most recent cryo-EM structures of membrane proteins and listed which detergents were utilized in their structure determination.

The results from this analysis provide many interesting insights. Once again we see the utility of Amphipol A8-35 for cryo-EM; however, to our knowledge, the structure of the ERAD-associated E3 ubiquitin-protein ligase HRD1 is the first example of the Amphipol PMAL-C8 being used for cryo-EM(8). Similarly, the structure GLP-1 receptor in complex with G protein(9) utilizes the detergent GDN, a synthetic and chemically similar substitute to Digitonin(10). Another interesting observation is the use of the fluorinated surfactants, octyl maltoside and fos-choline-8, to improve the vitrification process. 

Tools for Cryo-EM


We are excited to offer new tools for Cryo-EM from Molecular Dimensions which allow for easy and efficient storage and shipping of Cryo-EM samples. Our new Cryo-EM grid boxes can hold up to four grids in individually numbered positions. Our Cryo-EM grid box storage pucks are fully compatible with Uni-puck canisters and tools, and allow for quick and reliable identification of samples.

Recent membrane protein Cryo- EM Structures determined in 2017 (sorted by PDB release date)
 

PDB Release Date Name Ref. Resolution (Å) MW (kDa) Topology Detergent
5XTE 2017-08-30 Human respiratory complex III 11 3.40 497 α 0.1% Digitonin
5V6P 2017-08-16 HRD1 8 4.10 96 α Amphipol PMAL C8
0.1 mg/ml yeast polar lipid extract
5O8O 2017-08-16 TOM core complex 12 6.80 38 ß Non-ionic amphipol
5XSY 2017-08-09 Nav1.4-ß1 2 4.00 235 α 0.1% Digitonin
5WEO 2017-08-02 Activated GluA2 complex 13 4.20 464 α 0.05% Digitonin
5VOT 2017-07-12 GluA2-AMPA : TARP γ2 Complex 3 4.90 542 α 0.1% Digitonin
5VKQ 2017-06-28 NOMPC TRP channel 14 3.55 779 α MSP2N2 Nanodiscs
5VOX 2017-06-21 Yeast V-ATPase : SidK complex 15 6.80 1151 α 0.03% DDM
5O66 2017-06-14 AcrABZ-TolC 16 5.90 759 α Amphipol A8-35
5NJ3 2017-06-07 ABCG2 Multidrug Transporter 4 3.78 243 α MSP1D1 Nanodiscs
5NL2 2017-06-07 mTMEM16A ion channel 17 6.60 222 α 0.12% Digitonin
5VMS 2017-06-07 KCNQ1 channel 18 3.70 80 α 0.05% / 0.005% DDM : CHS
5XJY 2017-06-07 ABCA1 Lipid Exporter 19 4.10 262 α 0.06% Digitonin
5VAI 2017-05-24 GLP1 : G Protein Complex 9 4.10 162 α 0.01% LMNG / 0.01% GDN / 0.00192% POPG / 0.0012% Cholesterol
5VA1 2017-05-03 Human ERG K+ channel 5 3.70 89 α 0.025% / 0.005% DDM : CHS
5V4S 2017-04-12 Cyclic Nucleotide-Gated Ion Channel 20 4.20 214 α 50 uM LMNG / 5uM CHS
5LY6 2017-04-05 Membrane pore complex 21 4.50 53 ß Amphipol A8-35
5UOW 2017-03-22 Triheteromeric NMDA receptor 6 4.50 412 α 0.5 mM DDM
5X0M 2017-03-08 NavPaS Na channel 22 3.80 188 α 0.1% Digitonin
5UJ9 2017-02-22 MRP1 23 3.49 160 α 0.06% Digitonin
3 mM Fluorinated FC-8 added to improve vitrification
5U76 2017-02-08 Chicken Slo2.2 24 3.76 137 α 1.5 mM DDM
0.05 mg/ml POPE:POPG (3:1)
5H3O 2017-01-25 Eukaryotic cyclic nucleotide-gated channel 25 3.50 339 α Amphipol A8-35
5U6O 2017-01-25 Human HCN1 26 3.50 299 α 0.05% Digitonin
5MKE 2017-01-18 Polycystin-2 27 4.30 450 α Amphipol A8-35
5UAK 2017-01-18 CFTR 7 3.87 171 α 0.06% Digitonin
3 mM Fluorinated FC-8 added to improve vitrification
5TR1 2017-01-11 CLC-K chloride channel 28 3.95 197 α 0.04% / 0.004% DDM : CHS
5U1D 2017-01-11 Human TAP ATP-Binding Cassette Transporter 29 3.97 167 α 1 mM DDM
1 mM C12E8

References:
  1. Data obtained from RCSB PDB.
  2. Yan, Z., et al. Cell 170(3), 470-482.
  3. Chen, S., et al. Cell 170(6), 1234-1246.
  4. Taylor, N. M. I. et al. Nature 546(7659), 504-509.
  5. Wang, W. and MacKinnon, R. Cell 169(3), 422-430.
  6. Lü, W., et al. Science 355(6331), pii: eaal3729. doi: 10.1126/science.aal3729. Epub 2017 Feb 23.
  7. Liu, F., et al. Cell 169(1), 85-95.
  8. Schoebel, S., et al. Nature 548(7667), 352-355.
  9. Zhang, Y., et al. Nature 546(7657), 248-253.
  10. Chae, P. S., et al. Chemistry 18(31), 9485-9490.
  11. Guo, R., et al. Cell 170(6), 1247-1257.
  12. Bausewein, T., et al. Cell 170(4), 693-700.
  13. Twomey, E. C., et al. Nature 549(7670), 60-65.
  14. Jin, P., et al. Nature 547(7661), 118-122.
  15. Zhao, J., et al. PLoS Pathog 13(6), e1006394. doi: 10.1371/journal.ppat.1006394. eCollection 2017 Jun.
  16. Wang, Z., et al. Elife 6, pii: e24905. doi: 10.7554/eLife.24905.
  17. Paulino, C., et al. Elife 6, pii: e26232. doi: 10.7554/eLife.26232.
  18. Sun, J. and MacKinnon, R. Cell 169(6), 1042-1050.
  19. Qian, H., et al. Cell 169(7), 1228-1239.
  20. James, Z. M., et al. Proc Natl Acad Sci USA 114(17), 4430-4435.
  21. van Pee, K, et al. Elife 6, pii: e23644. doi: 10.7554/eLife.23644.
  22. Shen, H., et al. Science 355(6328), pii: eaal4326. doi: 10.1126/science.aal4326. Epub 2017 Feb 9.
  23. Johnson, Z. L. and Chen, J. Cell 168(6), 1075-1085.
  24. Hite, R. K. and MacKinnon, R. Cell 168(3), 390-399.
  25. Li, M. et al. Nature 542(7639), 60-65.
  26. Lee, C. H. and MacKinnon, R. Cell 168(1-2), 111-120.
  27. Wilkes, M. et al. Nat Struct. Mol Biol 24(2), 123-130.
  28. Park, E., et al. Nature 541(7638), 500-505.
  29. Oldham, M. L. et al. Elife: 5, pii: e21829. doi: 10.7554/eLife.21829.