Gamma-secretase cryo-EM structures

Resource availability

This page was written by Sjors Scheres to facilitate rapid dissemination of the results obtained in his group on cryo-EM structures of the human gamma-secretase complex. The cryo-EM reconstructions and atomic models described below can be downloaded here:

bioRxiv preprint: of our non-peer-reviewed draft (submitted for publication) on the apo-state ensemble and DAPT-bound structure

movie1.mp4 and movie2.mp4 as referred to in the draft, and illustrating the conformational differences between the different apo-state classes

apo_class1.mrc and apo_class1.pdb for the 1st class from the apo-state ensemble

apo_class2.mrc and apo_class2.pdb for the 2nd class from the apo-state ensemble

apo_class3.mrc and apo_class3.pdb for the 3rd class from the apo-state ensemble

dapt.mrc and dapt.pdb for the DAPT-bound structure

Please acknowledge our work if you use these resources, and do let us know if you have any useful feedback, in particular on the unpublished story of the apo-state ensemble and the DAPT-bound structure.

June 2014: a 4.5 Angstrom structure

In June 2014, we published a 4.5 Angstrom cryo-EM structure of human gamma-secretase. The corresponding publication (Lu, Bai, Ma et al. Nature 512, 166-170) is available for free from Pubmed Central. The cryo-EM map is available from the EMDB, the atomic model from the PDB.

This structure revealed structural homology of the nicastrin ectodomain to the carboxypeptidase PSMA. Nineteen helices were identified to adopt a horse-shoe-like arrangement in the transmembrane domain. Unfortunately, the limited resolution of our map precluded the assignment which of these helices correspond to each of the four proteins that make up gamma-secretase (nicastrin, Aph-1, presenilin and Pen-2).

April 2015: a 3.4 Angstrom structure

Earlier this year, improved image acquisition and processing led to the determination of the same structure at a resolution of 3.4 Angstrom. This structure allowed us to propose a near-complete model of this intriguing enzyme. The corresponding paper (by Bai, Yan, Yang et al) is now available online at Nature. The cryo-EM map is available from the EMDB, the atomic model from the PDB. Our earlier (non-peer-reviewed) interpretation of these results can also be downloaded here.

The high-resolution structure provides the first atomic-level insights into the gamma-secretase complex. It reveals two clusters of hotspots for FAD-mutations, and how sugars on the heavily glycosylated ectodomain of nicastrin stabilize a lid that covers its substrate-binding site. Ordered phospholipids stabilize the complex inside the membrane, where Aph-1 acts as a scaffold that holds a remarkably flexible active site in presenilin (on the outside of the horseshoe-shaped transmembrane domain) underneath the nicastrin ectodomain.

July 2015: sampling the conformational space of presenilin

Most recently, we have developed a new image classification procedure in RELION that allowed the identification of three sub-states in the data set that yielded the 3.4 Angstrom structure. These three structures reveal how transmembrane helices 2 and 6 of presenilin adopt multiple conformations in the apo-state ensemble. Furthermore, a structure in complex with the dipeptidic inhibitor DAPT shows how the flexibility of the catalytic subunit is strongly reduced upon inhibitor binding. Combined, these results form the basis for a new hypothesis of how gamma-secretase binds and cleaves its substrate. The paper has now been submitted for publication. A draft can be downloaded from bioRxiv.