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- PDB-9kqn: Hsp90-Cdc37-PINK1 complex -

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Basic information

Entry
Database: PDB / ID: 9kqn
TitleHsp90-Cdc37-PINK1 complex
Components
  • Heat shock protein HSP 90-alpha
  • Hsp90 co-chaperone Cdc37
  • Serine/threonine-protein kinase PINK1, mitochondrial
KeywordsCHAPERONE / Hsp90 / PINK1 / Cdc37 / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


positive regulation of synaptic transmission, dopaminergic / positive regulation of free ubiquitin chain polymerization / positive regulation of cristae formation / regulation of type II interferon-mediated signaling pathway / regulation of protein targeting to mitochondrion / mitochondrion to lysosome vesicle-mediated transport / HSP90-CDC37 chaperone complex / maintenance of protein location in mitochondrion / establishment of protein localization to mitochondrion / protein kinase B binding ...positive regulation of synaptic transmission, dopaminergic / positive regulation of free ubiquitin chain polymerization / positive regulation of cristae formation / regulation of type II interferon-mediated signaling pathway / regulation of protein targeting to mitochondrion / mitochondrion to lysosome vesicle-mediated transport / HSP90-CDC37 chaperone complex / maintenance of protein location in mitochondrion / establishment of protein localization to mitochondrion / protein kinase B binding / cellular response to hydrogen sulfide / 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 / protein kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase 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 / positive regulation of protein targeting to mitochondrion / regulation of reactive oxygen species metabolic process / positive regulation of ubiquitin-protein transferase activity / peptidase activator activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / astrocyte projection / vRNP Assembly / post-transcriptional regulation of gene expression / UTP binding / positive regulation of mitochondrial fission / negative regulation of macroautophagy / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / negative regulation of mitophagy / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / FOXO-mediated transcription of cell death genes / 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 / regulation of type I interferon-mediated signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / protein import into mitochondrial matrix / 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 / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of protein-containing complex assembly / HSF1 activation / negative regulation of mitochondrial fission / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / protein targeting / regulation of postsynaptic membrane neurotransmitter receptor levels / RHOBTB2 GTPase cycle
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
ADENOSINE-5'-DIPHOSPHATE / Heat shock protein HSP 90-alpha / 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: 2.84 Å
AuthorsTian, X.Y. / Su, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: To Be Published
Title: Human Hsp90-Cdc37-PINK1 complex
Authors: Tian, X.Y. / Su, J.Y.
History
DepositionNov 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)269,1216
Polymers268,2674
Non-polymers8542
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 Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP 86 / HSP86 / Heat shock protein family C member 1 / Lipopolysaccharide- ...Heat shock 86 kDa / HSP 86 / HSP86 / Heat shock protein family C member 1 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


Mass: 84781.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P07900, non-chaperonin molecular chaperone ATPase
#2: Protein Serine/threonine-protein kinase PINK1, mitochondrial / BRPK / PTEN-induced putative kinase protein 1


Mass: 54081.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PINK1 / Production host: Homo sapiens (human)
References: UniProt: Q9BXM7, non-specific serine/threonine protein kinase
#3: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16543
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
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: Hsp90-Cdc37-PINK1 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.277 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R0.6/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1324869 / Symmetry type: POINT

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