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- PDB-7u69: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -

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Basic information

Entry
Database: PDB / ID: 7u69
TitleCrystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Phenethyl Piperidine-4-acrylhydroxamic Acid Inhibitor
ComponentsPolyamine deacetylase HDAC10
KeywordsHYDROLASE/INHIBITOR / Histone Deacetylase / HYDROLASE-HYDROLASE INHIBITOR complex / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior ...polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior / epigenetic regulation of gene expression / macroautophagy / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / Chem-LS6 / PHOSPHATE ION / Polyamine deacetylase HDAC10
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHerbst-Gervasoni, C.J. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM49758 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Identification of histone deacetylase 10 (HDAC10) inhibitors that modulate autophagy in transformed cells.
Authors: Zeyen, P. / Zeyn, Y. / Herp, D. / Mahmoudi, F. / Yesiloglu, T.Z. / Erdmann, F. / Schmidt, M. / Robaa, D. / Romier, C. / Ridinger, J. / Herbst-Gervasoni, C.J. / Christianson, D.W. / Oehme, I. ...Authors: Zeyen, P. / Zeyn, Y. / Herp, D. / Mahmoudi, F. / Yesiloglu, T.Z. / Erdmann, F. / Schmidt, M. / Robaa, D. / Romier, C. / Ridinger, J. / Herbst-Gervasoni, C.J. / Christianson, D.W. / Oehme, I. / Jung, M. / Kramer, O.H. / Sippl, W.
History
DepositionMar 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyamine deacetylase HDAC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7598
Polymers75,0561
Non-polymers7037
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.389, 80.389, 247.514
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyamine deacetylase HDAC10 / Histone deacetylase 10


Mass: 75055.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac10 / Production host: Escherichia coli (E. coli)
References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase

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Non-polymers , 5 types, 120 molecules

#2: Chemical ChemComp-LS6 / (2E)-N-hydroxy-3-[1-(2-phenylethyl)piperidin-4-yl]prop-2-enamide


Mass: 274.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.1 M Sodium Phosphate Monobasic, 0.1 M Sodium Phosphate Dibasic, and 20% PEG 3350. Microseed crystals of HDAC10-Tubastatin were also added to the drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→69.68 Å / Num. obs: 31956 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.42 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.091 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2 / Num. unique obs: 3211 / CC1/2: 0.594 / Rpim(I) all: 0.584

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5td7

5td7


Resolution: 2.5→69.68 Å / SU ML: 0.3271 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 2011 6.3 %
Rwork0.1812 29913 -
obs0.1846 31924 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→69.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 38 113 4912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794911
X-RAY DIFFRACTIONf_angle_d0.97216705
X-RAY DIFFRACTIONf_chiral_restr0.0532777
X-RAY DIFFRACTIONf_plane_restr0.0053865
X-RAY DIFFRACTIONf_dihedral_angle_d5.69423911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.33331410.25412112X-RAY DIFFRACTION98.47
2.56-2.630.31451440.23862147X-RAY DIFFRACTION98.07
2.63-2.710.28641430.22352131X-RAY DIFFRACTION98.57
2.71-2.80.24381460.22392140X-RAY DIFFRACTION97.69
2.8-2.90.28061410.22132117X-RAY DIFFRACTION97.03
2.9-3.010.27091350.21882033X-RAY DIFFRACTION93.77
3.01-3.150.28521440.2132158X-RAY DIFFRACTION98.12
3.15-3.320.25341490.20762163X-RAY DIFFRACTION98.09
3.32-3.520.21751440.19092141X-RAY DIFFRACTION97.86
3.52-3.80.23471460.16482142X-RAY DIFFRACTION96.66
3.8-4.180.20971370.15522125X-RAY DIFFRACTION95.6
4.18-4.780.21161420.13842084X-RAY DIFFRACTION93.22
4.78-6.020.20121430.15822191X-RAY DIFFRACTION96.13
6.02-69.620.20671560.1692229X-RAY DIFFRACTION92.62

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