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- PDB-1t67: Crystal Structure of Human HDAC8 complexed with MS-344 -

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Basic information

Entry
Database: PDB / ID: 1t67
TitleCrystal Structure of Human HDAC8 complexed with MS-344
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / histone deacetylase / zinc hydrolase
Function / homology
Function and homology information


histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex ...histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / epigenetic regulation of gene expression / 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 / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / 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
Chem-B3N / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsSomoza, J.R. / Skene, R.J. / Katz, B.A. / Mol, C. / Ho, J.D. / Jennings, A.J. / Luong, C. / Arvai, A. / Buggy, J.J. / Chi, E. ...Somoza, J.R. / Skene, R.J. / Katz, B.A. / Mol, C. / Ho, J.D. / Jennings, A.J. / Luong, C. / Arvai, A. / Buggy, J.J. / Chi, E. / Tang, J. / Sang, B.-C. / Verner, E. / Wynands, R. / Leahy, E.M. / Dougan, D.R. / Snell, G. / Navre, M. / Knuth, M.W. / Swanson, R.V. / McRee, D.E. / Tari, L.W.
CitationJournal: Structure / Year: 2004
Title: Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases
Authors: Somoza, J.R. / Skene, R.J. / Katz, B.A. / Mol, C. / Ho, J.D. / Jennings, A.J. / Luong, C. / Arvai, A. / Buggy, J.J. / Chi, E. / Tang, J. / Sang, B.-C. / Verner, E. / Wynands, R. / Leahy, E.M. ...Authors: Somoza, J.R. / Skene, R.J. / Katz, B.A. / Mol, C. / Ho, J.D. / Jennings, A.J. / Luong, C. / Arvai, A. / Buggy, J.J. / Chi, E. / Tang, J. / Sang, B.-C. / Verner, E. / Wynands, R. / Leahy, E.M. / Dougan, D.R. / Snell, G. / Navre, M. / Knuth, M.W. / Swanson, R.V. / McRee, D.E. / Tari, L.W.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_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_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_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.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2215
Polymers41,8021
Non-polymers4194
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.644, 80.644, 105.523
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

#1: Protein Histone deacetylase 8 / HDAC8


Mass: 41802.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastbacHTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q9BY41
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-B3N / 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide / M344


Mass: 307.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: PEG 8000, HEPES, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 18, 2001 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→69 Å / Num. all: 17160 / Num. obs: 16130 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 30
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1610 / Rsym value: 0.55 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T64

1t64


Resolution: 2.31→69.01 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.762 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.397 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27368 869 5.1 %RANDOM
Rwork0.21247 ---
obs0.215 16130 94.91 %-
all-17160 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å21.8 Å20 Å2
2--3.6 Å20 Å2
3----5.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.31→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 25 137 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212787
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9573777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.425355
X-RAY DIFFRACTIONr_chiral_restr0.0810.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022144
X-RAY DIFFRACTIONr_nbd_refined0.1940.21500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2146
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.210
X-RAY DIFFRACTIONr_mcbond_it0.3371.51765
X-RAY DIFFRACTIONr_mcangle_it0.63122809
X-RAY DIFFRACTIONr_scbond_it1.06231022
X-RAY DIFFRACTIONr_scangle_it1.6614.5968
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 62
Rwork0.33 1147
Refinement TLS params.Method: refined / Origin x: 51.342 Å / Origin y: 0.909 Å / Origin z: 17.099 Å
111213212223313233
T0.2826 Å20.0952 Å20.0339 Å2-0.0437 Å20.0542 Å2--0.2062 Å2
L1.6449 °2-0.9014 °2-0.6882 °2-3.5614 °20.9748 °2--3.6797 °2
S0.0239 Å °0.2042 Å °0.0772 Å °0.0481 Å °-0.206 Å °-0.2941 Å °0.2705 Å °0.139 Å °0.1821 Å °

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