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- PDB-6pzo: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6pzo
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with YX-153
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Histone deacetylase / metallohydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process ...Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding / response to stress / hematopoietic progenitor cell differentiation / transferase activity / actin binding / chromatin organization / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytoplasm / cytosol
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 domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain ...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 domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-P6Y / Protein deacetylase HDAC6 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOsko, J.D. / 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: J.Med.Chem. / Year: 2020
Title: Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6.
Authors: Osko, J.D. / Porter, N.J. / Narayana Reddy, P.A. / Xiao, Y.C. / Rokka, J. / Jung, M. / Hooker, J.M. / Salvino, J.M. / Christianson, D.W.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hdac6 protein
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,41610
Polymers79,4502
Non-polymers9668
Water11,818656
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2085
Polymers39,7251
Non-polymers4834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2085
Polymers39,7251
Non-polymers4834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.810, 92.580, 96.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 39724.973 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 290-646)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli)
References: UniProt: A7YT55, UniProt: F8W4B7*PLUS, histone deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-P6Y / N-{[4-(hydroxycarbamoyl)phenyl]methyl}-2-(trifluoromethyl)pyridine-3-carboxamide


Mass: 339.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12F3N3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.65 % / Description: thick plate-like crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL zCD2 protein, 2 mM YX-153 inhibitor, 0.2 M succinic acid, pH 7.0, 20% w/v PEG3350, 1:1 ratio protein to precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2018
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→66.88 Å / Num. obs: 107228 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.088 / Net I/σ(I): 6.5
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 1.566 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10523 / CC1/2: 0.998 / Rpim(I) all: 0.438

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 5EEM

5eem


Resolution: 1.5→66.88 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs10523 99.1 %
Refinement stepCycle: LAST / Resolution: 1.5→66.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 54 656 6224

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