[English] 日本語
Yorodumi
- PDB-9kox: human Hsp90-FKBP51-PINK1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kox
Titlehuman Hsp90-FKBP51-PINK1 complex
Components
  • Heat shock protein HSP 90-alpha
  • Peptidyl-prolyl cis-trans isomerase FKBP5
  • Serine/threonine-protein kinase PINK1, mitochondrial
KeywordsCHAPERONE / Hsp90 / PINK1 / FKBP51 / 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 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
ADENOSINE-5'-DIPHOSPHATE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.43 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-FKBP51-PINK1 complex
Authors: Tian, X.Y. / Tian, X.Y.
History
DepositionNov 21, 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: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Peptidyl-prolyl cis-trans isomerase FKBP5
B: Heat shock protein HSP 90-alpha
A: Heat shock protein HSP 90-alpha
C: Serine/threonine-protein kinase PINK1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,7896
Polymers274,9354
Non-polymers8542
Water00
1


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

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor- ...PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 51290.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: 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
#3: 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
#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 modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: human Hsp90-FKBP51-PINK1 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.28 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 mesh size: 400 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
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)

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229994 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00816541
ELECTRON MICROSCOPYf_angle_d1.04322257
ELECTRON MICROSCOPYf_dihedral_angle_d17.9392208
ELECTRON MICROSCOPYf_chiral_restr0.0542462
ELECTRON MICROSCOPYf_plane_restr0.0062842

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more