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- PDB-4qa6: Crystal structure of I243N/Y306F HDAC8 in complex with a tetrapep... -

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Basic information

Entry
Database: PDB / ID: 4qa6
TitleCrystal structure of I243N/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 / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / histone deacetylase activity / mitotic sister chromatid cohesion / nuclear chromosome / Notch-HLH transcription pathway ...histone decrotonylase activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / histone deacetylase activity / mitotic sister chromatid cohesion / 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: 2.053 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)88,61514
Polymers87,7934
Non-polymers82210
Water6,936385
1
A: Histone deacetylase 8
C: tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3087
Polymers43,8972
Non-polymers4115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-41 kcal/mol
Surface area14450 Å2
MethodPISA
2
B: Histone deacetylase 8
D: tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3087
Polymers43,8972
Non-polymers4115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-43 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.832, 85.071, 94.444
Angle α, β, γ (deg.)90.00, 97.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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

#1: Protein Histone deacetylase 8 / HD8


Mass: 43216.934 Da / Num. of mol.: 2 / Mutation: I243N, 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 , 5 types, 395 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 277 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), 15% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: 2.05→50 Å / Num. all: 50869 / Num. obs: 49982 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 16.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4819 / % possible all: 95.4

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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: 2.053→47.769 Å / SU ML: 0.24 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 2532 5.07 %random
Rwork0.1807 ---
obs0.1822 49953 98.25 %-
all-50871 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.71 Å2
Refinement stepCycle: LAST / Resolution: 2.053→47.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5753 0 44 385 6182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026025
X-RAY DIFFRACTIONf_angle_d0.6698188
X-RAY DIFFRACTIONf_dihedral_angle_d11.392191
X-RAY DIFFRACTIONf_chiral_restr0.044882
X-RAY DIFFRACTIONf_plane_restr0.0031053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0534-2.09290.31661400.26142511X-RAY DIFFRACTION94
2.0929-2.13560.29361490.23692579X-RAY DIFFRACTION97
2.1356-2.1820.25681400.22932594X-RAY DIFFRACTION98
2.182-2.23280.25411370.23052599X-RAY DIFFRACTION98
2.2328-2.28860.28461460.21022601X-RAY DIFFRACTION98
2.2886-2.35050.27741610.21592603X-RAY DIFFRACTION98
2.3505-2.41970.23431300.20162623X-RAY DIFFRACTION98
2.4197-2.49770.2711460.20052635X-RAY DIFFRACTION98
2.4977-2.5870.26231460.19862633X-RAY DIFFRACTION99
2.587-2.69060.24021400.18642626X-RAY DIFFRACTION98
2.6906-2.8130.22281230.19662634X-RAY DIFFRACTION99
2.813-2.96130.23381230.1922677X-RAY DIFFRACTION99
2.9613-3.14680.2261530.19012638X-RAY DIFFRACTION99
3.1468-3.38970.19691450.18582659X-RAY DIFFRACTION99
3.3897-3.73070.1951170.16972703X-RAY DIFFRACTION99
3.7307-4.27030.17571280.15572683X-RAY DIFFRACTION99
4.2703-5.37890.16811630.14162674X-RAY DIFFRACTION100
5.3789-47.7820.15321450.1512749X-RAY DIFFRACTION100

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