title: A Near-Atomic Structure of the Dark Apoptosome Provides Insight into Assembly and Activation.
abstract: In Drosophila, the Apaf-1-related killer (Dark) forms an apoptosome that activates procaspases. To investigate function, we have determined a near-atomic structure of Dark double rings using cryo-electron microscopy. We then built a nearly complete model of the apoptosome that includes 7- and 8-blade β-propellers. We find that the preference for dATP during Dark assembly may be governed by Ser325, which is in close proximity to the 2' carbon of the deoxyribose ring. Interestingly, β-propellers in V-shaped domains of the Dark apoptosome are more widely separated, relative to these features in the Apaf-1 apoptosome. This wider spacing may be responsible for the lack of cytochrome c binding to β-propellers in the Dark apoptosome. Our structure also highlights the roles of two loss-of-function mutations that may block Dark assembly. Finally, the improved model provides a framework to understand apical procaspase activation in the intrinsic cell death pathway.
authors.affiliation: Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
authors.forename: Tat Cheung
authors.initials: TC
authors.lastname: Cheng
authors.affiliation: Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
authors.forename: Ildikó V
authors.initials: IV
authors.lastname: Akey
authors.affiliation: Department of Biologics Research - Protein Sciences, U.S. Innovation Center, Bayer Healthcare, 455 Mission Bay Boulevard South, San Francisco, CA 94158, USA.
authors.forename: Shujun
authors.initials: S
authors.lastname: Yuan
authors.affiliation: Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
authors.forename: Zhiheng
authors.initials: Z
authors.lastname: Yu
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Ludtke
authors.affiliation: Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA. Electronic address: cakey@bu.edu.
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Akey
mesh_terms: D000818:Animals; D017209:Apoptosis; D053478:Apoptosomes / Q000737:chemistry / Q000378:metabolism; D020169:Caspases / Q000378:metabolism; D020285:Cryoelectron Microscopy; D003838:Deoxyadenine Nucleotides / Q000378:metabolism*; D029721:Drosophila Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012694:Serine / Q000378:metabolism
chemical_list: D053478:Apoptosomes; D003838:Deoxyadenine Nucleotides; D029721:Drosophila Proteins; C400550:dark protein, Drosophila; D012694:Serine; D020169:Caspases; C026600:2'-deoxyadenosine triphosphate
keywords: apoptosis; apoptosome; procaspase activation; programmed cell death; single particle cryo-EM