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- EMDB-66567: Cryo-EM structure of HSP90-CDC37-PINK1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-66567
TitleCryo-EM structure of HSP90-CDC37-PINK1 complex
Map datasharp
Sample
  • Complex: tetrameric complex of PINK1 with an HSP90 dimer and CDC37
    • Protein or peptide: Hsp90 co-chaperone Cdc37
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
    • Protein or peptide: Heat shock protein HSP 90-beta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordschaperone / kinase / protein complex / PROTEIN BINDING
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
Heat shock protein HSP 90-beta / Hsp90 co-chaperone Cdc37 / Serine/threonine-protein kinase PINK1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsOkatsu K / Fukai S
Funding support Japan, 3 items
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, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66567.png

Downloads & links

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Map

FileDownload / File: emd_66567.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 240 pix.
= 173.76 Å		0.72 Å/pix.
x 240 pix.
= 173.76 Å		0.72 Å/pix.
x 240 pix.
= 173.76 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.724 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.6719141 - 1.3630235
Average (Standard dev.)0.0011426038 (±0.030405441)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 173.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66567_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Half map: #1

Fileemd_66567_half_map_2.map
Projections & Slices
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Sample components

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Entire : tetrameric complex of PINK1 with an HSP90 dimer and CDC37

EntireName: tetrameric complex of PINK1 with an HSP90 dimer and CDC37
Components
  • Complex: tetrameric complex of PINK1 with an HSP90 dimer and CDC37
    • Protein or peptide: Hsp90 co-chaperone Cdc37
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
    • Protein or peptide: Heat shock protein HSP 90-beta
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: tetrameric complex of PINK1 with an HSP90 dimer and CDC37

SupramoleculeName: tetrameric complex of PINK1 with an HSP90 dimer and CDC37
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hsp90 co-chaperone Cdc37

MacromoleculeName: Hsp90 co-chaperone Cdc37 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.622363 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVDYSVWDHI EV(SEP)DDEDETH PNIDTASLFR WRHQARVERM EQFQKEKEEL DRGCRECKRK VAECQRKLKE LEVAEG GKA ELERLQAEAQ QLRKEERSWE QKLEEMRKKE KSMPWNVDTL SKDGFSKSMV NTKPEKTEED SEEVREQKHK TFVEKYE KQ IKHFGMLRRW ...String:
MVDYSVWDHI EV(SEP)DDEDETH PNIDTASLFR WRHQARVERM EQFQKEKEEL DRGCRECKRK VAECQRKLKE LEVAEG GKA ELERLQAEAQ QLRKEERSWE QKLEEMRKKE KSMPWNVDTL SKDGFSKSMV NTKPEKTEED SEEVREQKHK TFVEKYE KQ IKHFGMLRRW DDSQKYLSDN VHLVCEETAN YLVIWCIDLE VEEKCALMEQ VAHQTIVMQF ILELAKSLKV DPRACFRQ F FTKIKTADRQ YMEGFNDELE AFKERVRGRA KLRIEKAMKE YEEEERKKRL GPGGLDPVEV YESLPEELQK CFDVKDVQM LQDAISKMDP TDAKYHMQRC IDSGLWVPNS KASEAKEGEE AGPGDPLLEA VPKTGDEKDV SV

UniProtKB: Hsp90 co-chaperone Cdc37

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Macromolecule #2: Serine/threonine-protein kinase PINK1, mitochondrial

MacromoleculeName: Serine/threonine-protein kinase PINK1, mitochondrial / type: protein_or_peptide / ID: 2 / Details: C-terminal His8-tag / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.05427 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGLGLGLIEE KQAESRRAVS ACQEIQAIFT QKSKPGPDPL DTRRLQGFRL EEYLIGQSIG KGCSAAVYEA TMPTLPQNLE VTKSTGLLP GRGPGTSAPG EGQERAPGAP AFPLAIKMMW NISAGSSSEA ILNTMSQELV PASRVALAGE YGAVTYRKSK R GPKQLAPH ...String:
MGLGLGLIEE KQAESRRAVS ACQEIQAIFT QKSKPGPDPL DTRRLQGFRL EEYLIGQSIG KGCSAAVYEA TMPTLPQNLE VTKSTGLLP GRGPGTSAPG EGQERAPGAP AFPLAIKMMW NISAGSSSEA ILNTMSQELV PASRVALAGE YGAVTYRKSK R GPKQLAPH PNIIRVLRAF TSSVPLLPGA LVDYPDVLPS RLHPEGLGHG RTLFLVMKNY PCTLRQYLCV NTPSPRLAAM ML LQLLEGV DHLVQQGIAH RDLKSDNILV ELDPDGCPWL VIADFGCCLA DESIGLQLPF SSWYVDRGGN GCLMAPEVST ARP GPRAVI DYSKADAWAV GAIAYEIFGL VNPFYGQGKA HLESRSYQEA QLPALPESVP PDVRQLVRAL LQREASKRPS ARVA ANVLH LSLWGEHILA LKNLKLDKMV GWLLQQSAAT LLANRLTEKC CVETKMKMLF LANLECETLC QAALLLCSWR AALHH HHHH HH

UniProtKB: Serine/threonine-protein kinase PINK1, mitochondrial

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Macromolecule #3: Heat shock protein HSP 90-beta

MacromoleculeName: Heat shock protein HSP 90-beta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.38425 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPEEVHHGEE EVETFAFQAE IAQLMSLIIN TFYSNKEIFL RELISNASDA LDKIRYESLT DPSKLDSGKE LKIDIIPNPQ ERTLTLVDT GIGMTKADLI NNLGTIAKSG TKAFMEALQA GADISMIGQF GVGFYSAYLV AEKVVVITKH NDDEQYAWES S AGGSFTVR ...String:
MPEEVHHGEE EVETFAFQAE IAQLMSLIIN TFYSNKEIFL RELISNASDA LDKIRYESLT DPSKLDSGKE LKIDIIPNPQ ERTLTLVDT GIGMTKADLI NNLGTIAKSG TKAFMEALQA GADISMIGQF GVGFYSAYLV AEKVVVITKH NDDEQYAWES S AGGSFTVR ADHGEPIGRG TKVILHLKED QTEYLEERRV KEVVKKHSQF IGYPITLYLE KEREKEISDD EAEEEKGEKE EE DKDDEEK PKIEDVGSDE EDDSGKDKKK KTKKIKEKYI DQEELNKTKP IWTRNPDDIT QEEYGEFYKS LTNDWEDHLA VKH FSVEGQ LEFRALLFIP RRAPFDLFEN KKKKNNIKLY VRRVFIMDSC DELIPEYLNF IRGVVDSEDL PLNISREMLQ QSKI LKVIR KNIVKKCLEL FSELAEDKEN YKKFYEAFSK NLKLGIHEDS TNRRRLSELL RYHTSQSGDE MTSLSEYVSR MKETQ KSIY YITGESKEQV ANSAFVERVR KRGFEVVYMT EPIDEYCVQQ LKEFDGKSLV SVTKEGLELP EDEEEKKKME ESKAKF ENL CKLMKEILDK KVEKVTISNR LVSSPCCIVT STYGWTANME RIMKAQALRD NSTMGYMMAK KHLEINPDHP IVETLRQ KA EADKNDKAVK DLVVLLFETA LLSSGFSLED PQTHSNRIYR MIKLGLGIDE DEVAAEEPNA AVPDEIPPLE GDEDASRM E EVD

UniProtKB: Heat shock protein HSP 90-beta

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.67 mg/mL
BufferpH: 8
Details: 50mM Tris-HCl pH 8.0, 150mM NaCl, 10mM MgCl2, 10mM KCl, 20mM Na2MoO4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7z38

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 454727
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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