Evaluation: A pseudoatomic model of the COPII cage

I evaluated this paper for F1000 Prime:

Noble AJ, Zhang Q, O’Donnell J, Hariri H, Bhattacharya N, Marshall AG, Stagg SM. (2013) A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry. Nature Structural and Molecular Biology 20(2):167-73

This paper describes a technical tour de force that elucidates some of the finer detail of the molecular structure of the assembled COPII coat. The Stagg lab have obtained a 12-Å structure of the human COPII cage from cryo-electron microscopy and layered on top of this data from hydrogen deuterium exchange (HDX) experiments to define the flexible regions of the assembled structure. The structure was made possible in part by a neat gradient fixation protocol to isolate assembled cages from aggregated material (GraFix, described in (Kastner et al., 2008)). Molecular dynamics flexible fitting of the previous crystallographic structure of the Sec13-31 complex to the EM data provided clear insight into the formation of the vertex elements of the assembled coat. Specifically, the authors demonstrate that Sec13-Sec31 unit has an intrinsic “polarity” within the assembled coat with one end tightly packed and the pother more loosely integrated. This resulted in the identification of a further contact site at the vertex region that reveals a less significant role for Sec13 and a greater contact area through Sec31 than has been previously suggested (Stagg et al., 2008). This has the potential to explain data that suggest that the requirement for Sec13 in vivo is not as stringent as one might expect ((Copic et al., 2012; Townley et al., 2008)). The loose packing evident within the edge element of the Sec31 alpha-solenoid could flex to accommodate unusually large cargo. Overall, this paper is impressive from a technical perspective as well as for the insight it provides into COPII assembly.

Copic, A., C.F. Latham, M.A. Horlbeck, J.G. D’Arcangelo, and E.A. Miller. 2012. ER cargo properties specify a requirement for COPII coat rigidity mediated by Sec13p. Science. 335:1359-1362.

Kastner, B., N. Fischer, M.M. Golas, B. Sander, P. Dube, D. Boehringer, K. Hartmuth, J. Deckert, F. Hauer, E. Wolf, H. Uchtenhagen, H. Urlaub, F. Herzog, J.M. Peters, D. Poerschke, R. Luhrmann, and H. Stark. 2008. GraFix: sample preparation for single-particle electron cryomicroscopy. Nature methods. 5:53-55.

Stagg, S.M., P. LaPointe, A. Razvi, C. Gurkan, C.S. Potter, B. Carragher, and W.E. Balch. 2008. Structural basis for cargo regulation of COPII coat assembly. Cell. 134:474-484.

Townley, A.K., Y. Feng, K. Schmidt, D.A. Carter, R. Porter, P. Verkade, and D.J. Stephens. 2008. Efficient coupling of Sec23-Sec24 to Sec13-Sec31 drives COPII-dependent collagen secretion and is essential for normal craniofacial development. J. Cell Sci. 121:3025-3034.