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- PDB-9k91: Cryo-EM structure of human histone deacetylase 6 tandem catalytic... -

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Basic information

Entry
Database: PDB / ID: 9k91
TitleCryo-EM structure of human histone deacetylase 6 tandem catalytic domain (HDAC6 CD1-2)
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / Deacetylase / Metalloenzyme
Function / homology
Function and homology information


negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / Cargo trafficking to the periciliary membrane / negative regulation of aggrephagy / response to misfolded protein / positive regulation of protein oligomerization / type 2 mitophagy / negative regulation of protein-containing complex disassembly / peroxidase inhibitor activity ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / Cargo trafficking to the periciliary membrane / negative regulation of aggrephagy / response to misfolded protein / positive regulation of protein oligomerization / type 2 mitophagy / negative regulation of protein-containing complex disassembly / peroxidase inhibitor activity / regulation of autophagy of mitochondrion / tubulin deacetylation / deacetylase activity / Transcriptional regulation by RUNX2 / tubulin deacetylase activity / lysosome localization / cilium disassembly / ATPase inhibitor activity / protein deacetylation / misfolded protein binding / positive regulation of type 2 mitophagy / cytoplasmic ubiquitin ligase complex / regulation of androgen receptor signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / aggresome assembly / Transferases; Acyltransferases; Aminoacyltransferases / aggresome / histone deacetylase activity / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / microtubule associated complex / Notch-HLH transcription pathway / axonal transport of mitochondrion / RUNX2 regulates osteoblast differentiation / regulation of microtubule-based movement / negative regulation of gene expression, epigenetic / histone deacetylase complex / cell leading edge / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of epithelial cell migration / dynein complex binding / cilium assembly / regulation of macroautophagy / HSF1 activation / polyubiquitin modification-dependent protein binding / alpha-tubulin binding / negative regulation of protein-containing complex assembly / beta-tubulin binding / negative regulation of proteolysis / multivesicular body / axon cytoplasm / inclusion body / transcription corepressor binding / regulation of autophagy / ubiquitin binding / regulation of protein stability / Hsp90 protein binding / intracellular protein transport / Late endosomal microautophagy / caveola / beta-catenin binding / protein destabilization / NOTCH1 Intracellular Domain Regulates Transcription / tau protein binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cellular response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / histone deacetylase binding / Chaperone Mediated Autophagy / Aggrephagy / ubiquitin protein ligase activity / cellular response to heat / actin binding / microtubule binding / microtubule / perikaryon / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / dendrite / perinuclear region of cytoplasm / enzyme binding / DNA-templated transcription / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Protein deacetylase HDAC6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsSun, C. / Xie, K. / Zhu, Z. / Chao, Y. / Zhou, Z. / Qu, Q. / Zhu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371227 China
National Natural Science Foundation of China (NSFC)32171194 China
CitationJournal: To Be Published
Title: Hydrogen sulfide binds to the zinc-active-site of hHDAC6 to increase enzyme activity via an H2S-mediated deacetylation pathway
Authors: Sun, C. / Wang, Y. / Cai, S. / Xie, K. / Li, M. / Zhu, Z. / Chao, Y. / Zhou, Z. / Chen, Y. / Xue, W. / Mu, X. / Bian, X. / Miao, W. / Wu, J. / Ding, Q. / Wang, M. / Tao, B. / Zhang, I. / ...Authors: Sun, C. / Wang, Y. / Cai, S. / Xie, K. / Li, M. / Zhu, Z. / Chao, Y. / Zhou, Z. / Chen, Y. / Xue, W. / Mu, X. / Bian, X. / Miao, W. / Wu, J. / Ding, Q. / Wang, M. / Tao, B. / Zhang, I. / Zhu, Y. / Qu, Q. / Zhu, Y.
History
DepositionOct 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data 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: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2663
Polymers84,1351
Non-polymers1312
Water00
1


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

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Components

#1: Protein Histone deacetylase 6 / HD6 / Protein deacetylase HDAC6 / Tubulin-lysine deacetylase HDAC6


Mass: 84135.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Histone deacetylase 6 tandem catalytic domain CD1-2.
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC6, KIAA0901, JM21 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q9UBN7, histone deacetylase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Human HDAC6 catalytic domain (CD1-2) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 3500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.2.0particle selection
2EPU3.0.0.4164RELimage acquisition
4cryoSPARCv4.2.0CTF correction
7UCSF ChimeraXversion 1.5model fitting
9cryoSPARCv4.2.0initial Euler assignment
10cryoSPARCv4.2.0final Euler assignment
11cryoSPARCv4.2.0classification
12cryoSPARCv4.2.03D reconstruction
13PHENIX1.20.1_4487:model refinement
Image processingDetails: 14937 EER movies were collected,beam-induced motion was corrected by Relion.
CTF correctionDetails: CTF parameters were estimated using patchCTF in cryoSPARC.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 12675859
Details: 2 rounds of blob picking were conducted to generate auto-picking templates, then a final round of template-based auto-picking was conducted. Selected particles were extracted and grouped ...Details: 2 rounds of blob picking were conducted to generate auto-picking templates, then a final round of template-based auto-picking was conducted. Selected particles were extracted and grouped according to 2D classification.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109995 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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