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- EMDB-62482: human Hsp90-FKBP51-PINK1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-62482
Titlehuman Hsp90-FKBP51-PINK1 complex
Map data
Sample
  • Complex: human Hsp90-FKBP51-PINK1 complex
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP5
    • Protein or peptide: Heat shock protein HSP 90-alpha
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHsp90 / PINK1 / FKBP51 / CYTOSOLIC PROTEIN / CHAPERONE
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 protein targeting to mitochondrion / mitochondrion to lysosome vesicle-mediated transport / maintenance of protein location in mitochondrion / establishment of protein localization to mitochondrion / protein kinase B binding / cellular response to hydrogen sulfide / Lewy body ...positive regulation of synaptic transmission, dopaminergic / positive regulation of free ubiquitin chain polymerization / positive regulation of cristae formation / regulation of protein targeting to mitochondrion / mitochondrion to lysosome vesicle-mediated transport / 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 hydrogen peroxide metabolic process / regulation of oxidative phosphorylation / 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 / cellular response to toxic substance / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrion organization / Modulation of host responses by IFN-stimulated genes / response to alcohol / negative regulation of JNK cascade / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of reactive oxygen species metabolic process / peptidase activator activity / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / astrocyte projection / vRNP Assembly / UTP binding / positive regulation of mitochondrial fission / negative regulation of macroautophagy / sperm plasma membrane / FK506 binding / chaperone-mediated autophagy / negative regulation of mitophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / 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 / FOXO-mediated transcription of cell death genes / 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 / negative regulation of reactive oxygen species metabolic process / hemopoiesis / 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 / negative regulation of mitochondrial fission / HSF1 activation / regulation of protein-containing complex assembly / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / axonal growth cone / neurofibrillary tangle assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / RHOBTB2 GTPase cycle / mitophagy / MECP2 regulates neuronal receptors and channels / positive regulation of lamellipodium assembly
Similarity search - Function
PINK1, protein kinase domain / : / : / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 ...PINK1, protein kinase domain / : / : / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain 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 / Peptidyl-prolyl cis-trans isomerase FKBP5 / Serine/threonine-protein kinase PINK1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.43 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-FKBP51-PINK1 complex
Authors: Tian XY / Tian XY
History
DepositionNov 21, 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_62482.png

Downloads & links

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Map

FileDownload / File: emd_62482.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
AxesZ (Sec.)Y (Row.)X (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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8697 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.109
Minimum - Maximum-0.73143023 - 1.252463
Average (Standard dev.)0.00043763162 (±0.038236633)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_62482_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62482_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : human Hsp90-FKBP51-PINK1 complex

EntireName: human Hsp90-FKBP51-PINK1 complex
Components
  • Complex: human Hsp90-FKBP51-PINK1 complex
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP5
    • Protein or peptide: Heat shock protein HSP 90-alpha
    • Protein or peptide: Serine/threonine-protein kinase PINK1, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: human Hsp90-FKBP51-PINK1 complex

SupramoleculeName: human Hsp90-FKBP51-PINK1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP5

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.290191 KDa
SequenceString: MTTDEGAKNN EESPTATVAE QGEDITSKKD RGVLKIVKRV GNGEETPMIG DKVYVHYKGK LSNGKKFDSS HDRNEPFVFS LGKGQVIKA WDIGVATMKK GEICHLLCKP EYAYGSAGSL PKIPSNATLF FEIELLDFKG EDLFEDGGII RRTKRKGEGY S NPNEGATV ...String:
MTTDEGAKNN EESPTATVAE QGEDITSKKD RGVLKIVKRV GNGEETPMIG DKVYVHYKGK LSNGKKFDSS HDRNEPFVFS LGKGQVIKA WDIGVATMKK GEICHLLCKP EYAYGSAGSL PKIPSNATLF FEIELLDFKG EDLFEDGGII RRTKRKGEGY S NPNEGATV EIHLEGRCGG RMFDCRDVAF TVGEGEDHDI PIGIDKALEK MQREEQCILY LGPRYGFGEA GKPKFGIEPN AE LIYEVTL KSFEKAKESW EMDTKEKLEQ AAIVKEKGTV YFKGGKYMQA VIQYGKIVSW LEMEYGLSEK ESKASESFLL AAF LNLAMC YLKLREYTKA VECCDKALGL DSANEKGLYR RGEAQLLMNE FESAKGDFEK VLEVNPQNKA ARLQISMCQK KAKE HNERD RRIYANMFKK FAEQDAKEEA NKAMGKKTSE GVTNEKGTDS QAMEEEKPEG HV

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP5

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Macromolecule #2: Heat shock protein HSP 90-alpha

MacromoleculeName: Heat shock protein HSP 90-alpha / type: protein_or_peptide / ID: 2 / 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 #3: Serine/threonine-protein kinase PINK1, mitochondrial

MacromoleculeName: Serine/threonine-protein kinase PINK1, mitochondrial / type: protein_or_peptide / ID: 3 / 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 #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 / Mesh: 400
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: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 229994
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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