3IYG

Ca model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map

Summary for 3IYG

• Entry DOI: 10.2210/pdb3iyg/pdb
• Related: 3KTT
• EMDB information: 5145 5148
• Descriptor: T-complex protein 1 subunit theta, T-complex protein 1 subunit gamma, T-complex protein 1 subunit zeta, ... (8 entities in total)
• Functional Keywords: tric/cct, asymmetric, cryo-em, subunit arrangement, atp-binding, chaperone, isopeptide bond, nucleotide-binding, phosphoprotein, disulfide bond
• Biological source: Bos taurus (bovine); More
• Total number of polymer chains: 8
• Total formula weight: 451949.00

Authors

Cong, Y.,Baker, M.L.,Ludtke, S.J.,Frydman, J.,Chiu, W. (deposition date: 2009-11-28, release date: 2010-03-16, Last modification date: 2024-02-21)

Primary citation

Cong, Y.,Baker, M.L.,Jakana, J.,Woolford, D.,Miller, E.J.,Reissmann, S.,Kumar, R.N.,Redding-Johanson, A.M.,Batth, T.S.,Mukhopadhyay, A.,Ludtke, S.J.,Frydman, J.,Chiu, W.
4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.
Proc.Natl.Acad.Sci.USA, 107:4967-4972, 2010

PubMed Abstract: The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7-A resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-A resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Calpha backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed approximately 95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity.

PubMed: 20194787
DOI: 10.1073/pnas.0913774107

Experimental method

ELECTRON MICROSCOPY (4 Å)