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- PDB-6oin: Crystal structure of MYST acetyltransferase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6oin
TitleCrystal structure of MYST acetyltransferase domain in complex with inhibitor CTX-124143
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Complex / MYST / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


MSL complex / histone H4K16 acetyltransferase activity / regulation of mRNA processing / myeloid cell differentiation / NSL complex / : / peptide-lysine-N-acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex ...MSL complex / histone H4K16 acetyltransferase activity / regulation of mRNA processing / myeloid cell differentiation / NSL complex / : / peptide-lysine-N-acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / neurogenesis / regulation of autophagy / transcription coregulator activity / kinetochore / nuclear matrix / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily ...MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-MQJ / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHermans, S.J. / Chung, M.C. / Parker, M.W. / Thomas, T. / Baell, J.B.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Benzoylsulfonohydrazides as Potent Inhibitors of the Histone Acetyltransferase KAT6A.
Authors: Leaver, D.J. / Cleary, B. / Nguyen, N. / Priebbenow, D.L. / Lagiakos, H.R. / Sanchez, J. / Xue, L. / Huang, F. / Sun, Y. / Mujumdar, P. / Mudududdla, R. / Varghese, S. / Teguh, S. / Charman, ...Authors: Leaver, D.J. / Cleary, B. / Nguyen, N. / Priebbenow, D.L. / Lagiakos, H.R. / Sanchez, J. / Xue, L. / Huang, F. / Sun, Y. / Mujumdar, P. / Mudududdla, R. / Varghese, S. / Teguh, S. / Charman, S.A. / White, K.L. / Katneni, K. / Cuellar, M. / Strasser, J.M. / Dahlin, J.L. / Walters, M.A. / Street, I.P. / Monahan, B.J. / Jarman, K.E. / Sabroux, H.J. / Falk, H. / Chung, M.C. / Hermans, S.J. / Parker, M.W. / Thomas, T. / Baell, J.B.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6424
Polymers32,1401
Non-polymers5023
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.340, 56.730, 121.790
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 Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 32140.057 Da / Num. of mol.: 1 / Fragment: residues 176-448 / Mutation: A142S, L145M, T146I, K157R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7Z6, histone acetyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MQJ / 2-fluoro-N'-[(naphthalen-2-yl)sulfonyl]benzohydrazide


Mass: 344.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13FN2O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 2% Tacsimate pH 7.0, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→121.79 Å / Num. obs: 36070 / % possible obs: 99.78 % / Redundancy: 7.5 % / Rpim(I) all: 0.029 / Net I/σ(I): 16
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3539 / Rpim(I) all: 0.19 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→121.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.065 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22048 1802 5 %RANDOM
Rwork0.19722 ---
obs0.1984 34268 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.105 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.61 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.7→121.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 31 99 2384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022438
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3541.9723323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87923.628113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8215424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0921512
X-RAY DIFFRACTIONr_chiral_restr0.1810.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211872
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 123 -
Rwork0.255 2294 -
obs--100 %

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