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- PDB-4qa5: Crystal structure of A188T/Y306F HDAC8 in complex with a tetrapep... -

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Basic information

Entry
Database: PDB / ID: 4qa5
TitleCrystal structure of A188T/Y306F HDAC8 in complex with a tetrapeptide substrate
Components
  • Histone deacetylase 8
  • tetrapeptide substrate
KeywordsHYDROLASE / metalloenzyme / histone deacetylase / enzyme substrate complex / Cornelia de Lange Syndrome / arginase/deacetylase fold
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 / negative regulation of protein ubiquitination / Hsp70 protein binding / 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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 7-AMINO-4-METHYL-CHROMEN-2-ONE / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDecroos, C. / Bowman, C.B. / Moser, J.-A.S. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders.
Authors: Decroos, C. / Bowman, C.M. / Moser, J.A. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 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

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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: tetrapeptide substrate
D: tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,60614
Polymers87,8524
Non-polymers75410
Water11,277626
1
A: Histone deacetylase 8
C: tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3618
Polymers43,9262
Non-polymers4356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-43 kcal/mol
Surface area15080 Å2
MethodPISA
2
B: Histone deacetylase 8
D: tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2456
Polymers43,9262
Non-polymers3194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-46 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.830, 97.760, 105.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein Histone deacetylase 8 / HD8


Mass: 43246.016 Da / Num. of mol.: 2 / Mutation: A188T, Y306F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide tetrapeptide substrate


Mass: 679.811 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide

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Non-polymers , 6 types, 636 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-MCM / 7-AMINO-4-METHYL-CHROMEN-2-ONE / 7-AMINO-4-METHYLCOUMARIN


Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M tris(hydroxymethyl)aminomethane) (TRIS, pH = 8.0), 4 mM tris(2-carboxyethyl)phosphine (TCEP), 8% PEG 35000, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 85490 / Num. obs: 85478 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 19.5
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1370)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EWF

3ewf


Resolution: 1.76→46.418 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / σ(F): 1.33 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 4274 5.01 %
Rwork0.1674 --
obs0.1687 85387 99.94 %
all-85431 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.19 Å2
Refinement stepCycle: LAST / Resolution: 1.76→46.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 39 626 6479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066172
X-RAY DIFFRACTIONf_angle_d1.0688400
X-RAY DIFFRACTIONf_dihedral_angle_d12.6932263
X-RAY DIFFRACTIONf_chiral_restr0.072907
X-RAY DIFFRACTIONf_plane_restr0.0051086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7599-1.77990.31641570.25692633X-RAY DIFFRACTION99
1.7799-1.80090.25941580.24012661X-RAY DIFFRACTION100
1.8009-1.82280.29021370.22442657X-RAY DIFFRACTION100
1.8228-1.84590.25971230.21322696X-RAY DIFFRACTION100
1.8459-1.87020.26561430.20222664X-RAY DIFFRACTION100
1.8702-1.89580.25431450.19932656X-RAY DIFFRACTION100
1.8958-1.92290.22271550.20482680X-RAY DIFFRACTION100
1.9229-1.95160.23991220.19642700X-RAY DIFFRACTION100
1.9516-1.98210.23851420.1952662X-RAY DIFFRACTION100
1.9821-2.01460.22151360.19582666X-RAY DIFFRACTION100
2.0146-2.04930.26211280.19742707X-RAY DIFFRACTION100
2.0493-2.08660.23571450.18122685X-RAY DIFFRACTION100
2.0866-2.12670.22381510.18542702X-RAY DIFFRACTION100
2.1267-2.17010.22521180.1852680X-RAY DIFFRACTION100
2.1701-2.21730.21581240.17512729X-RAY DIFFRACTION100
2.2173-2.26890.22961570.17812651X-RAY DIFFRACTION100
2.2689-2.32560.19291360.17162711X-RAY DIFFRACTION100
2.3256-2.38850.18421440.1712690X-RAY DIFFRACTION100
2.3885-2.45880.21121330.16942697X-RAY DIFFRACTION100
2.4588-2.53820.20991370.16942697X-RAY DIFFRACTION100
2.5382-2.62890.19341650.17032700X-RAY DIFFRACTION100
2.6289-2.73410.20091320.16042711X-RAY DIFFRACTION100
2.7341-2.85850.20381520.16912719X-RAY DIFFRACTION100
2.8585-3.00920.18211380.16562705X-RAY DIFFRACTION100
3.0092-3.19770.19261380.16852744X-RAY DIFFRACTION100
3.1977-3.44450.16831450.16732727X-RAY DIFFRACTION100
3.4445-3.7910.17961430.14972753X-RAY DIFFRACTION100
3.791-4.33930.13651550.13532738X-RAY DIFFRACTION100
4.3393-5.46560.17711460.13962794X-RAY DIFFRACTION100
5.4656-46.4340.15991690.14952898X-RAY DIFFRACTION100

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