Mechanism of folding chamber closure in a group II chaperonin.
Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.
Zhang
Junjie
J
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
Baker
Matthew L
ML
Schröder
Gunnar F
GF
Douglas
Nicholai R
NR
Reissmann
Stefanie
S
Jakana
Joanita
J
Dougherty
Matthew
M
Fu
Caroline J
CJ
Levitt
Michael
M
Ludtke
Steven J
SJ
Frydman
Judith
J
Chiu
Wah
W
D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D000494:Allosteric Regulation; D001665:Binding Sites; D020285:Cryoelectron Microscopy; D056385:Group II Chaperonins / Q000737:chemistry* / Q000378:metabolism* / Q000648:ultrastructure; D006868:Hydrolysis / Q000187:drug effects; D017017:Methanococcus / Q000737:chemistry*; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation / Q000187:drug effects; D017510:Protein Folding; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship
D021122:Protein Subunits; D000255:Adenosine Triphosphate; D056385:Group II Chaperonins