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- PDB-7jvv: Crystal structure of human histone deacetylase 8 (HDAC8) E66D/Y30... -

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Basic information

Entry
Database: PDB / ID: 7jvv
TitleCrystal structure of human histone deacetylase 8 (HDAC8) E66D/Y306F double mutation complexed with a tetrapeptide substrate
Components
  • ACE-ARG-HIS-ALY-ALY-MCM
  • Histone deacetylase 8
KeywordsHYDROLASE / Histone deacetylase / Cornelia de Lange Syndrome (CdLS)
Function / homology
Function and homology information


histone decrotonylase activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / regulation of telomere maintenance / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway ...histone decrotonylase activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / regulation of telomere maintenance / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / Hsp70 protein binding / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / HDACs deacetylate histones / Hsp90 protein binding / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Separation of Sister Chromatids / heterochromatin formation / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Histone deacetylase / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsOsko, J.D. / Christianson, D.W. / Decroos, C. / Porter, N.J. / Lee, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural analysis of histone deacetylase 8 mutants associated with Cornelia de Lange Syndrome spectrum disorders.
Authors: Osko, J.D. / Porter, N.J. / Decroos, C. / Lee, M.S. / Watson, P.R. / Raible, S.E. / Krantz, I.D. / Deardorff, M.A. / Christianson, D.W.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 8
B: Histone deacetylase 8
C: ACE-ARG-HIS-ALY-ALY-MCM
D: ACE-ARG-HIS-ALY-ALY-MCM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,04620
Polymers88,0784
Non-polymers96816
Water8,053447
1
A: Histone deacetylase 8
C: ACE-ARG-HIS-ALY-ALY-MCM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,52310
Polymers44,0392
Non-polymers4848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-28 kcal/mol
Surface area13990 Å2
MethodPISA
2
B: Histone deacetylase 8
D: ACE-ARG-HIS-ALY-ALY-MCM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,52310
Polymers44,0392
Non-polymers4848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-27 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.048, 97.470, 104.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Histone deacetylase 8 / HD8


Mass: 43201.965 Da / Num. of mol.: 2 / Mutation: E66D/Y306F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide ACE-ARG-HIS-ALY-ALY-MCM


Mass: 836.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 463 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris, pH 8.0, 20% PEG6000, 4 mM TCEP

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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: Aug 15, 2015
RadiationMonochromator: Cryogenically-cooled 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: 1.84→45.97 Å / Num. obs: 72663 / % possible obs: 97.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.052 / Net I/σ(I): 13.8
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 70664 / CC1/2: 0.759 / Rpim(I) all: 0.355 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EWF

3ewf


Resolution: 1.84→45.97 Å / SU ML: 0.196 / Cross valid method: FREE R-VALUE / σ(F): 1.338 / Phase error: 19.064
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.197 3536 5.008 %
Rwork0.164 --
obs0.166 70609 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5648 0 50 447 6145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065896
X-RAY DIFFRACTIONf_angle_d0.818003
X-RAY DIFFRACTIONf_dihedral_angle_d7.5334621
X-RAY DIFFRACTIONf_chiral_restr0.053873
X-RAY DIFFRACTIONf_plane_restr0.0061030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.845-1.86960.29381390.24182547X-RAY DIFFRACTION93
1.8696-1.89630.271530.22992679X-RAY DIFFRACTION100
1.8963-1.92460.2691340.22232707X-RAY DIFFRACTION99
1.9246-1.95470.26791450.21212713X-RAY DIFFRACTION99
1.9547-1.98670.26931410.20042682X-RAY DIFFRACTION99
1.9867-2.0210.20551430.18862681X-RAY DIFFRACTION99
2.021-2.05770.21791400.17792730X-RAY DIFFRACTION98
2.0577-2.09730.21011260.17822690X-RAY DIFFRACTION99
2.0973-2.14010.21061400.17352712X-RAY DIFFRACTION98
2.1401-2.18670.21611560.17092627X-RAY DIFFRACTION98
2.1867-2.23750.21521330.16652722X-RAY DIFFRACTION98
2.2375-2.29350.19561620.15922653X-RAY DIFFRACTION98
2.2935-2.35550.21161420.16472682X-RAY DIFFRACTION98
2.3555-2.42480.23781350.16722671X-RAY DIFFRACTION97
2.4248-2.50310.21051370.16342697X-RAY DIFFRACTION97
2.5031-2.59250.22851330.16392661X-RAY DIFFRACTION97
2.5925-2.69630.18551300.15752695X-RAY DIFFRACTION97
2.6963-2.8190.18931500.16422655X-RAY DIFFRACTION97
2.819-2.96760.21661410.1662681X-RAY DIFFRACTION97
2.9676-3.15350.19721430.16292682X-RAY DIFFRACTION96
3.1535-3.39690.20151380.16412679X-RAY DIFFRACTION97
3.3969-3.73860.1891550.15392679X-RAY DIFFRACTION96
3.7386-4.27930.1421510.13472664X-RAY DIFFRACTION96
4.2793-5.39010.14261280.13872722X-RAY DIFFRACTION95
5.3901-45.960.16821410.15782762X-RAY DIFFRACTION93

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