Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin

Abstract

Protein folding is assisted by molecular chaperones. CCT (chaperonin containing TCP-1, or TRiC) is a 1-MDa oligomer that is built by two rings comprising eight different 60-kDa subunits. This chaperonin regulates the folding of important proteins including actin, α-tubulin and β-tubulin. We used an electron density map at 5.5 Å resolution to reconstruct CCT, which showed a substrate in the inner cavities of both rings. Here we present the crystal structure of the open conformation of this nanomachine in complex with tubulin, providing information about the mechanism by which it aids tubulin folding. The structure showed that the substrate interacts with loops in the apical and equatorial domains of CCT. The organization of the ATP-binding pockets suggests that the substrate is stretched inside the cavity. Our data provide the basis for understanding the function of this chaperonin.

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Figure 1: Scheme of the overall model of CCT containing two copies of each of the eight subunits α, β, γ, ζ, ɛ, δ, θ and η.
Figure 2: Apical domain conformations.
Figure 3: Interaction between tubulin and CCT.
Figure 4: Detailed view of the ATP binding pockets.
Figure 5: Silencing and complementation assays to analyze the function of the sensor and apical loops in the CCT-β subunit in HEK293 cells.

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Acknowledgements

We thank the Swiss Light Source and European Synchrotron Radiation Facility beamline staff for their support. Funding was obtained through Ministerio de Ciencia e Innovación (MICINN) grants BFU2008-01344/BMC to G.M., BFU2007-62382/BMC to J.M.V. and CSD2006-20642 to G.M. and J.M.V., Comunidad Autónoma de Madrid grants CAM-P2006/Gen-0166 to G.M. and S2009MAT-1507 to J.M.V., and EU 3D-Repertoire grants LSHG-CT-2005-512028 to G.M., J.M.V., M.Z. and C.V.R. and HEALTH-F4-2008-201648 to C.V.R. M.M. acknowledges the financial support of SAF2009-07973 and CSD2007-00017 (MICINN) and S-BIO-0283-2006 (CAM).

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Contributions

H.Y. and A.B. isolated the complex, I.G.M. and H.Y. obtained the crystals, I.G.M. and G.M. solved the structure, H.Y. and J.M.V. performed the cryo-EM, H.Y. and M.Z. carried out the protease digestion and substrate cleaning experiments, M.Z., A.Y.P. and C.V.R. performed the mass spectrometry and proteomic analysis, P.M., G.d.C., E.B.-N., M.M. and M.S. performed the shRNA assay, all the authors analyzed the data and J.M.V. and G.M. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to José M Valpuesta or Guillermo Montoya.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Notes, Supplementary Figures 1–11, Supplementary Table 1 and Supplementary Methods (PDF 2004 kb)

Supplementary Movie 1

CCT subunits conformational changes inside the ring. This movie summarizes the relative movements that take place inside one of the CCT rings (only the equatorial domain and part of the intermediate domain are shown here). One of the CCT subunits alternates between the different conformations present in the ring (all the other subunits were fitted on that position superimposing their structurally conserved equatorial domains). A dashed circle is depicted as a reference to display the variable sensor loop conformations, which apparently produce a retractile movement towards the centre of the CCT inner cavity (the frame sequence has been ordered to show this “movement”). This movie also depicts the relative movement of the intermediate domain with respect the equatorial domain, which produces the opening and closure of the nucleotide-binding site (here represented with an AMPPNP molecule modelled from the thermosome structure 1Q3Q). (MOV 1073 kb)

Supplementary Movie 2

The molecular forge. A combination of the different conformation of the CCT subunits has been mounted in a random sequence (each subunit varies between eight different resolved conformations; see Supplementary Movie 1) depicting a possible mechanism for CCT mediated folding. In this representation, the piston-like sensor loops modify the shape of a white rubber band that represents a theoretical substrate. If this substrate is bound to several sensor loops at the same time, the substrate could experience local compressions, expansions and torsions that force its folding process. This input of kinetic energy, driven by the ATP binding-hydrolysis cycles, would be used to overcome folding-pathway barriers. Eventually a properly folded product is obtained. (MOV 7014 kb)

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Muñoz, I., Yébenes, H., Zhou, M. et al. Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin. Nat Struct Mol Biol 18, 14–19 (2011). https://doi.org/10.1038/nsmb.1971

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