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- EMDB-62508: Hsp90-Cdc37-PINK1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62508
TitleHsp90-Cdc37-PINK1 complex
Map data
Sample
  • Complex: Hsp90-Cdc37-PINK1 complex
    • Protein or peptide: Heat shock protein HSP 90-alpha
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
    • Protein or peptide: Hsp90 co-chaperone Cdc37
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHsp90 / PINK1 / Cdc37 / CYTOSOLIC PROTEIN / CHAPERONE
Function / homology
Function and homology information


positive regulation of free ubiquitin chain polymerization / positive regulation of synaptic transmission, dopaminergic / positive regulation of cristae formation / regulation of type II interferon-mediated signaling pathway / : / mitochondrion to lysosome vesicle-mediated transport / HSP90-CDC37 chaperone complex / maintenance of protein location in mitochondrion / : / cellular response to hydrogen sulfide ...positive regulation of free ubiquitin chain polymerization / positive regulation of synaptic transmission, dopaminergic / positive regulation of cristae formation / regulation of type II interferon-mediated signaling pathway / : / mitochondrion to lysosome vesicle-mediated transport / HSP90-CDC37 chaperone complex / maintenance of protein location in mitochondrion / : / cellular response to hydrogen sulfide / protein kinase B binding / Lewy body / regulation of autophagy of mitochondrion / regulation of synaptic vesicle transport / TORC2 signaling / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of mitochondrial electron transport, NADH to ubiquinone / regulation of oxidative phosphorylation / regulation of hydrogen peroxide metabolic process / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / C3HC4-type RING finger domain binding / regulation of cellular response to oxidative stress / dopamine secretion / negative regulation of autophagosome assembly / positive regulation of dopamine secretion / autophagy of mitochondrion / positive regulation of type 2 mitophagy / regulation of cyclin-dependent protein serine/threonine kinase activity / protein kinase regulator activity / cellular response to toxic substance / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrion organization / protein folding chaperone complex / negative regulation of JNK cascade / regulation of reactive oxygen species metabolic process / : / peptidase activator activity / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein polymerization / Scavenging by Class F Receptors / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / vRNP Assembly / UTP binding / astrocyte projection / post-transcriptional regulation of gene expression / positive regulation of mitochondrial fission / negative regulation of macroautophagy / chaperone-mediated autophagy / sperm plasma membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / negative regulation of mitophagy / mitochondrial transport / telomerase holoenzyme complex assembly / FOXO-mediated transcription of cell death genes / Uptake and function of diphtheria toxin / 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 / negative regulation of intrinsic apoptotic signaling pathway / protein import into mitochondrial matrix / regulation of type I interferon-mediated signaling pathway / dendritic growth cone / TPR domain binding / positive regulation of release of cytochrome c from mitochondria / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / positive regulation of ATP biosynthetic process / hemopoiesis / negative regulation of reactive oxygen species metabolic process / positive regulation of macroautophagy / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / enzyme-substrate adaptor activity / response to unfolded protein / negative regulation of mitochondrial fission / skeletal muscle contraction / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / axonal growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels
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 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-alpha / Hsp90 co-chaperone Cdc37 / Serine/threonine-protein kinase PINK1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsTian XY / Su JY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: To Be Published
Title: Human Hsp90-Cdc37-PINK1 complex
Authors: Tian XY / Su JY
History
DepositionNov 26, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62508.png

Downloads & links

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Map

FileDownload / File: emd_62508.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.87 Å/pix.
x 280 pix.
= 243.516 Å		0.87 Å/pix.
x 280 pix.
= 243.516 Å		0.87 Å/pix.
x 280 pix.
= 243.516 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8697 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.62
Minimum - Maximum-17.762371000000002 - 40.238613000000001
Average (Standard dev.)0.0014395231 (±1.059026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 243.516 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Hsp90-Cdc37-PINK1 complex

EntireName: Hsp90-Cdc37-PINK1 complex
Components
  • Complex: Hsp90-Cdc37-PINK1 complex
    • Protein or peptide: Heat shock protein HSP 90-alpha
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
    • Protein or peptide: Hsp90 co-chaperone Cdc37
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Hsp90-Cdc37-PINK1 complex

SupramoleculeName: Hsp90-Cdc37-PINK1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 277 KDa

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Macromolecule #1: Heat shock protein HSP 90-alpha

MacromoleculeName: Heat shock protein HSP 90-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-chaperonin molecular chaperone ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.781727 KDa
SequenceString: MPEETQTQDQ PMEEEEVETF AFQAEIAQLM SLIINTFYSN KEIFLRELIS NSSDALDKIR YESLTDPSKL DSGKELHINL IPNKQDRTL TIVDTGIGMT KADLINNLGT IAKSGTKAFM EALQAGADIS MIGQFGVGFY SAYLVAEKVT VITKHNDDEQ Y AWESSAGG ...String:
MPEETQTQDQ PMEEEEVETF AFQAEIAQLM SLIINTFYSN KEIFLRELIS NSSDALDKIR YESLTDPSKL DSGKELHINL IPNKQDRTL TIVDTGIGMT KADLINNLGT IAKSGTKAFM EALQAGADIS MIGQFGVGFY SAYLVAEKVT VITKHNDDEQ Y AWESSAGG SFTVRTDTGE PMGRGTKVIL HLKEDQTEYL EERRIKEIVK KHSQFIGYPI TLFVEKERDK EVSDDEAEEK ED KEEEKEK EEKESEDKPE IEDVGSDEEE EKKDGDKKKK KKIKEKYIDQ EELNKTKPIW TRNPDDITNE EYGEFYKSLT NDW EDHLAV KHFSVEGQLE FRALLFVPRR APFDLFENRK KKNNIKLYVR RVFIMDNCEE LIPEYLNFIR GVVDSEDLPL NISR EMLQQ SKILKVIRKN LVKKCLELFT ELAEDKENYK KFYEQFSKNI KLGIHEDSQN RKKLSELLRY YTSASGDEMV SLKDY CTRM KENQKHIYYI TGETKDQVAN SAFVERLRKH GLEVIYMIEP IDEYCVQQLK EFEGKTLVSV TKEGLELPED EEEKKK QEE KKTKFENLCK IMKDILEKKV EKVVVSNRLV TSPCCIVTST YGWTANMERI MKAQALRDNS TMGYMAAKKH LEINPDH SI IETLRQKAEA DKNDKSVKDL VILLYETALL SSGFSLEDPQ THANRIYRMI KLGLGIDEDD PTADDTSAAV TEEMPPLE G DDDTSRMEEV D

UniProtKB: Heat shock protein HSP 90-alpha

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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 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.081094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LIEEKQAESR RAVSACQEIQ AIFTQKSKPG PDPLDTRRLQ GFRLEEYLIG QSIGKGCSAA VYEATMPTLP QNLEVTKSTG LLPGRGPGT SAPGEGQERA PGAPAFPLAI KMMWNISAGS SSEAILNTMS QELVPASRVA LAGEYGAVTY RKSKRGPKQL A PHPNIIRV ...String:
LIEEKQAESR RAVSACQEIQ AIFTQKSKPG PDPLDTRRLQ GFRLEEYLIG QSIGKGCSAA VYEATMPTLP QNLEVTKSTG LLPGRGPGT SAPGEGQERA PGAPAFPLAI KMMWNISAGS SSEAILNTMS QELVPASRVA LAGEYGAVTY RKSKRGPKQL A PHPNIIRV LRAFTSSVPL LPGALVDYPD VLPSRLHPEG LGHGRTLFLV MKNYPCTLRQ YLCVNTPSPR LAAMMLLQLL EG VDHLVQQ GIAHRDLKSD NILVELDPDG CPWLVIADFG CCLADESIGL QLPFSSWYVD RGGNGCLMAP EVSTARPGPR AVI DYSKAD AWAVGAIAYE IFGLVNPFYG QGKAHLESRS YQEAQLPALP ESVPPDVRQL VRALLQREAS KRPSARVAAN VLHL SLWGE HILALKNLKL DKMVGWLLQQ SAATLLANRL TEKCCVETKM KMLFLANLEC ETLCQAALLL CSWRAALDYK DHDGG YKDH DIDYKDDDDK

UniProtKB: Serine/threonine-protein kinase PINK1, mitochondrial

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Macromolecule #3: Hsp90 co-chaperone Cdc37

MacromoleculeName: Hsp90 co-chaperone Cdc37 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.622363 KDa
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 #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

BufferpH: 7.4
GridModel: Quantifoil R0.6/1 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1324869
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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