Structural basis for the folding of PINK1 by the HSP90–CDC37 chaperone complex

Kei Okatsu author has email address
Hayato Yamamoto
Akinori Okamoto
Shinya H Goto
Yumiko Nishimoto
Yukihiko Sugita
Takeshi Noda
Shuya Fukai author has email address

Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan

https://doi.org/10.7554/eLife.110255.1

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Figures and data

Cryo-EM structure of the PINK1–HSP90–CDC37 complex.
(a) Domain organizations of human PINK1, CDC37, and HSP90β. MTS, N-terminal mitochondrial targeting sequence; OMS, outer mitochondrial localization signal; TMD, transmembrane domain; CTE, C-terminal extension; NTD, N-terminal domain; MD, middle domain; CTD, C-terminal domain. The PINK1 kinase domain consisting of the N- and C-lobes is colored in pink, the CTE in magenta, CDC37 in green, and HSP90β in cyan. (b) Schematic diagram of the PINK1–HSP90–CDC37 complex. The coloring scheme is the same as in (a) except that the two HSP90β protomers are colored in cyan and blue. (c) Cryo-EM density map and structure of the PINK1–HSP90–CDC37 complex at 3.08 Å resolution. The coloring scheme is the same as in (b).

Data collection and refinement statistics

Interaction of the PINK1 C-lobe with CDC37 mediated by the loop of the N-terminal domain.
(a) Overall view of the cryo-EM structure of the PINK1–HSP90–CDC37 complex. The box indicates an area including the locations of the views shown in (b-e) (b) Close-up view of the density map at the interface between PINK1 (pink) and CDC37 (green). (c) Close-up view of the PINK1–CDC37 interaction around Trp31 of CDC37. The structure (top) and corresponding map (bottom) are shown. (d) Close-up view of the PINK1–CDC37 interaction around Ile23 of CDC37. The structure (top) and corresponding map (bottom) are shown. (e) Close-up view of the PINK1–CDC37 interaction around His31 of CDC37. The structure (top) and corresponding map (bottom) are shown. (f) Amino-acid sequence alignment of the PINK1 residues located at the CDC37-interacting interface among representative vertebrates. *, identical residues; :, residues with strongly similar properties; ., residues with weakly similar properties.

Comparison of the HPNI motif between CDC37 and PINK1.
(a) Comparison between the NTD^CDC37–C-lobe^PINK1 interaction (cryo-EM) and N-lobe^PINK1–C-lobe^PINK1 interaction (AlphaFold2). The boxes indicate the loop containing the HPNI motif. (b) Close-up view of the HPNI motifs of CDC37 (green; cryo-EM) and PINK1 (red; AlphaFold2). (c) Amino-acid sequence alignment of the HPNI motif-containing loop of human PINK1 and CDC37. *, identical residues; :, residues with strongly similar properties; ., residues with weakly similar properties. (d) Amino-acid sequence alignment of the HPNI motif-containing loop of PINK1 among representative vertebrates. *, identical residues; :, residues with strongly similar properties; ., residues with weakly similar properties.

Insertion of the β5 strand of the PINK1 N-lobe into the interfacial channel of the HSP90 dimer.
(a) The AlphaFold2-predicted model (AF-Q9BXM7-F1-model_v4) of human PINK1. The N-lobe contains the five-stranded β sheet (β1–β5). (b) Overall view of the cryo-EM structure of the PINK1–HSP90–CDC37 complex. (c) Close-up view of the unfolded segment of the PINK1 N-lobe, which is inserted into the channel at the interface between two protomers in the HSP90 dimer. (d, e) Close-up view of the density map and structures around the unfolded segment of the PINK1 N-lobe.

Interface between the PINK1 CTE and HSP90.
(a) The structure and density map of the interface between PINK1 and HSP90. The two boxes indicate the locations of the views shown in (c) and (d) (b) Superposition of the cryo-EM and AlphaFold2-predicted PINK1 structures. (c) Close-up view of the structure and density map around Trp312 of HSP90 and Leu539 of PINK1. (d) Close-up view of the interface between the PINK1 CTE and HSP90 FCL.

Comparison of the spatial arrangement of HSP90–CDC37 and TOM–VDAC relative to PINK1.
(a) Cryo-EM structure of the PINK1–TOM–VDAC complex (PDB 9EIH). (b) Close-up views of PINK1–TOM5–TOM20 in the PINK1–TOM–VDAC complex. The other components of the complex are omitted for clarity. (c) Comparison between the PINK1–TOM20 and PINK1–HSP90 interactions. In the PINK1–TOM20 interface (left panel), TOM20 interacts with both the PINK1 CTE and N-helix, which also interact with each other. In the PINK1–HSP90 interface (middle panel), the FCL^HSP90 covers the PINK1 CTE. The superposition (right panel) shows that the PINK1 N-helix and TOM20 overlap with the NTD^HSP90 and MD^HSP90. (d) Comparison between the PINK1–TOM5 and PINK1–HSP90 interactions. In the PINK1–TOM5 interface (left panel), the TOM5 interacts with the PINK1 CTE. The superposition (right panel) shows that TOM5 overlaps with the FCL^HSP90.

Model for PINK1 stabilization by the HSP90–CDC37 complex and transition to its active state on depolarized mitochondria.
(a) In the cytosol, the HSP90–CDC37 complex captures the folding intermediate of PINK1, where the N-lobe remains unfolded due to binding of the isolated β5 strand to HSP90, whereas the C-lobe and CTE is folded. The CTE is covered with FCL^HSP90. The HPNI motif of CDC37 interacts with the C-lobe of PINK1, mimicking the HPNI motif of the N-lobe. (b) TOM20 and TOM5 compete with HSP90–CDC37 for binding to the PINK1 CTE, displacing the chaperone complex from PINK1. (c) Upon mitochondrial depolarization, the dissociation of the HSP90–CDC37 complex allows the PINK1 CTE to interact with the N-helix and further with TOM20 and TOM5, along with the N-lobe folding. Finally, PINK1 dimerizes and becomes activated in a trans-autophosphorylation fashion.

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