3IYF

Atomic Model of the Lidless Mm-cpn in the Open State

Summary for 3IYF

• Entry DOI: 10.2210/pdb3iyf/pdb
• Related: 3IYE
• EMDB information: 5140
• Descriptor: Chaperonin (1 entity in total)
• Functional Keywords: group ii chaperonin, protein folding, mm-cpn, single particle reconstruction, methanococcus maripaludis, chaperone, atp-binding, nucleotide-binding
• Biological source: Methanococcus maripaludis
• Total number of polymer chains: 16
• Total formula weight: 889826.19

Authors

Zhang, J.,Baker, M.L.,Schroeder, G.,Douglas, N.R.,Reissmann, S.,Jakana, J.,Dougherty, M.,Fu, C.J.,Levitt, M.,Ludtke, S.J.,Frydman, J.,Chiu, W. (deposition date: 2009-10-23, release date: 2010-02-02, Last modification date: 2024-02-21)

Primary citation

Zhang, J.,Baker, M.L.,Schroder, G.F.,Douglas, N.R.,Reissmann, S.,Jakana, J.,Dougherty, M.,Fu, C.J.,Levitt, M.,Ludtke, S.J.,Frydman, J.,Chiu, W.
Mechanism of folding chamber closure in a group II chaperonin
Nature, 463:379-383, 2010

PubMed Abstract: 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.

PubMed: 20090755
DOI: 10.1038/nature08701

Experimental method

ELECTRON MICROSCOPY (8 Å)