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- EMDB-62184: Cryo-EM structure of human histone deacetylase 6 tandem catalytic... -

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Basic information

Entry
Database: EMDB / ID: EMD-62184
TitleCryo-EM structure of human histone deacetylase 6 tandem catalytic domain (HDAC6 CD1-2)
Map data
Sample
  • Complex: Human HDAC6 catalytic domain (CD1-2)
    • Protein or peptide: Histone deacetylase 6
  • Ligand: ZINC ION
KeywordsDeacetylase / Metalloenzyme / Hydrolase
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)
Methodsingle 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, 2 items
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 / Zhu Y / Qu Q / Zhu Y
History
DepositionOct 25, 2024-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62184.png

Downloads & links

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Map

FileDownload / File: emd_62184.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 200 pix.
= 186.4 Å		0.93 Å/pix.
x 200 pix.
= 186.4 Å		0.93 Å/pix.
x 200 pix.
= 186.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.123
Minimum - Maximum-0.72113127 - 0.92686856
Average (Standard dev.)0.0000012067542 (±0.027942222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 186.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62184_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62184_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_62184_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Human HDAC6 catalytic domain (CD1-2)

EntireName: Human HDAC6 catalytic domain (CD1-2)
Components
  • Complex: Human HDAC6 catalytic domain (CD1-2)
    • Protein or peptide: Histone deacetylase 6
  • Ligand: ZINC ION

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Supramolecule #1: Human HDAC6 catalytic domain (CD1-2)

SupramoleculeName: Human HDAC6 catalytic domain (CD1-2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone deacetylase 6

MacromoleculeName: Histone deacetylase 6 / type: protein_or_peptide / ID: 1
Details: Histone deacetylase 6 tandem catalytic domain CD1-2.
Number of copies: 1 / Enantiomer: LEVO / EC number: histone deacetylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.135336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SLEVLFQGPE LAGTGLVLDE QLNEFHCLWD DSFPEGPERL HAIKEQLIQE GLLDRCVSFQ ARFAEKEELM LVHSLEYIDL METTQYMNE GELRVLADTY DSVYLHPNSY SCACLASGSV LRLVDAVLGA EIRNGMAIIR PPGHHAQHSL MDGYCMFNHV A VAARYAQQ ...String:
SLEVLFQGPE LAGTGLVLDE QLNEFHCLWD DSFPEGPERL HAIKEQLIQE GLLDRCVSFQ ARFAEKEELM LVHSLEYIDL METTQYMNE GELRVLADTY DSVYLHPNSY SCACLASGSV LRLVDAVLGA EIRNGMAIIR PPGHHAQHSL MDGYCMFNHV A VAARYAQQ KHRIRRVLIV DWDVHHGQGT QFTFDQDPSV LYFSIHRYEQ GRFWPHLKAS NWSTTGFGQG QGYTINVPWN QV GMRDADY IAAFLHVLLP VALEFQPQLV LVAAGFDALQ GDPKGEMAAT PAGFAQLTHL LMGLAGGKLI LSLEGGYNLR ALA EGVSAS LHTLLGDPCP MLESPGAPCR SAQASVSCAL EALEPFWEVL VRSTETVERD NMEEDNVEES EEEGPWEPPV LPIL TWPVL QSRTGLVYDQ NMMNHCNLWD SHHPEVPQRI LRIMCRLEEL GLAGRCLTLT PRPATEAELL TCHSAEYVGH LRATE KMKT RELHRESSNF DSIYICPSTF ACAQLATGAA CRLVEAVLSG EVLNGAAVVR PPGHHAEQDA ACGFCFFNSV AVAARH AQT ISGHALRILI VDWDVHHGNG TQHMFEDDPS VLYVSLHRYD HGTFFPMGDE GASSQIGRAA GTGFTVNVAW NGPRMGD AD YLAAWHRLVL PIAYEFNPEL VLVSAGFDAA RGDPLGGCQV SPEGYAHLTH LLMGLASGRI ILILEGGYNL TSISESMA A CTRSLLGDPP PLLTLPRPPL SGALASITET IQVHRRYWRS LR

UniProtKB: Protein deacetylase HDAC6

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.6 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Details14937 EER movies were collected,beam-induced motion was corrected by Relion.
Particle selectionNumber 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.
CTF correctionSoftware - Name: cryoSPARC (ver. v4.2.0)
Details: CTF parameters were estimated using patchCTF in cryoSPARC.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: The startup model was generated by ab-initio in cryoSPARC.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.0) / Number images used: 109995
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 106609 / Software - Name: cryoSPARC (ver. v4.2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 50
Output model

PDB-9k91:
Cryo-EM structure of human histone deacetylase 6 tandem catalytic domain (HDAC6 CD1-2)

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