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- PDB-9x4x: Cryo-EM structure of HSP90-CDC37-PINK1 complex -

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Basic information

Entry
Database: PDB / ID: 9x4x
TitleCryo-EM structure of HSP90-CDC37-PINK1 complex
Components
  • Heat shock protein HSP 90-beta
  • Hsp90 co-chaperone Cdc37
  • Serine/threonine-protein kinase PINK1, mitochondrial
KeywordsPROTEIN BINDING / chaperone / kinase / protein complex
Function / homology
Function and homology information


positive regulation of cristae formation / positive regulation of free ubiquitin chain polymerization / regulation of type II interferon-mediated signaling pathway / regulation of protein localization to mitochondrion / mitochondrion to lysosome vesicle-mediated transport / maintenance of protein location in mitochondrion / protein kinase B binding / cellular response to hydrogen sulfide / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling ...positive regulation of cristae formation / positive regulation of free ubiquitin chain polymerization / regulation of type II interferon-mediated signaling pathway / regulation of protein localization to mitochondrion / mitochondrion to lysosome vesicle-mediated transport / maintenance of protein location in mitochondrion / protein kinase B binding / cellular response to hydrogen sulfide / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / regulation of autophagy of mitochondrion / positive regulation of mitochondrial electron transport, NADH to ubiquinone / regulation of oxidative phosphorylation / C3HC4-type RING finger domain binding / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of synaptic vesicle transport / aryl hydrocarbon receptor complex / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / negative regulation of autophagosome assembly / regulation of hydrogen peroxide metabolic process / regulation of cellular response to oxidative stress / histone methyltransferase binding / positive regulation of type 2 mitophagy / dynein axonemal particle / positive regulation of protein localization to cell surface / autophagy of mitochondrion / receptor ligand inhibitor activity / protein kinase regulator activity / negative regulation of mitophagy / cellular response to toxic substance / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of mitochondrion organization / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / ATP-dependent protein binding / TORC2 signaling / negative regulation of JNK cascade / negative regulation of reactive oxygen species metabolic process / regulation of reactive oxygen species metabolic process / peptidase activator activity / positive regulation of mitochondrial fission / post-transcriptional regulation of gene expression / HSP90-CDC37 chaperone complex / telomerase holoenzyme complex assembly / positive regulation of protein localization to mitochondrion / Respiratory syncytial virus genome replication / negative regulation of intrinsic apoptotic signaling pathway / FOXO-mediated transcription of cell death genes / astrocyte projection / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / Uptake and function of diphtheria toxin / regulation of type I interferon-mediated signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / hemopoiesis / dendritic growth cone / TPR domain binding / positive regulation of release of cytochrome c from mitochondria / Assembly and release of respiratory syncytial virus (RSV) virions / Lewy body / positive regulation of macroautophagy / positive regulation of ATP biosynthetic process / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / The NLRP3 inflammasome / response to unfolded protein / protein phosphatase activator activity / HSF1-dependent transactivation / protein localization to mitochondrion / regulation of protein-containing complex assembly / Attenuation phase / protein folding chaperone complex / HSF1 activation / protein targeting / negative regulation of macroautophagy / chaperone-mediated protein complex assembly / mitophagy / axonal growth cone / response to ischemia / telomere maintenance via telomerase / negative regulation of mitochondrial fission / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / Dengue virus activates/modulates innate and adaptive immune responses / heat shock protein binding / Signaling by ERBB2 / DNA polymerase binding / peptide binding / supramolecular fiber organization / protein folding chaperone / ESR-mediated signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process
Similarity search - Function
PINK1, protein kinase domain / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 ...PINK1, protein kinase domain / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 / Cdc37, N-terminal domain / Cdc37 N terminal kinase binding / : / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Heat shock protein HSP 90-beta / Hsp90 co-chaperone Cdc37 / Serine/threonine-protein kinase PINK1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsOkatsu, K. / Fukai, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K15084 Japan
Japan Society for the Promotion of Science (JSPS)24H01894 Japan
Japan Society for the Promotion of Science (JSPS)18H05501 Japan
CitationJournal: To Be Published
Title: Structural basis for the folding of PINK1 by the HSP90-CDC37 chaperone complex
Authors: Okatsu, K. / Yamamoto, H. / Okamoto, A. / Nishimoto, Y. / Fukai, S.
History
DepositionOct 12, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Hsp90 co-chaperone Cdc37
D: Serine/threonine-protein kinase PINK1, mitochondrial
A: Heat shock protein HSP 90-beta
B: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,5088
Polymers264,4454
Non-polymers1,0634
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Hsp90 co-chaperone Cdc37 / Hsp90 chaperone protein kinase-targeting subunit / p50Cdc37


Mass: 44622.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC37, CDC37A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16543
#2: Protein Serine/threonine-protein kinase PINK1, mitochondrial / BRPK / PTEN-induced putative kinase protein 1


Mass: 53054.270 Da / Num. of mol.: 1 / Fragment: residues 104-581 / Mutation: F104M
Source method: isolated from a genetically manipulated source
Details: C-terminal His8-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: PINK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BXM7, non-specific serine/threonine protein kinase
#3: Protein Heat shock protein HSP 90-beta / HSP 90 / Heat shock 84 kDa / HSP 84 / HSP84 / Heat shock protein family C member 3


Mass: 83384.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPC3, HSPCB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08238
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: tetrameric complex of PINK1 with an HSP90 dimer and CDC37
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Details: 50mM Tris-HCl pH 8.0, 150mM NaCl, 10mM MgCl2, 10mM KCl, 20mM Na2MoO4
SpecimenConc.: 0.67 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 190000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
5cryoSPARCCTF correction
11cryoSPARCfinal Euler assignment
13cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 454727 / Symmetry type: POINT
RefinementHighest resolution: 3.08 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00614335
ELECTRON MICROSCOPYf_angle_d0.82619291
ELECTRON MICROSCOPYf_dihedral_angle_d14.4965512
ELECTRON MICROSCOPYf_chiral_restr0.0582135
ELECTRON MICROSCOPYf_plane_restr0.0052456

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