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

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Basic information

Entry
Database: PDB / ID: 6owh
TitleCrystal structure of MYST acetyltransferase domain in complex with inhibitor 92
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Complex / MYST / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / dosage compensation by inactivation of X chromosome ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / dosage compensation by inactivation of X chromosome / post-embryonic hemopoiesis / myeloid cell differentiation / NSL complex / negative regulation of epithelial to mesenchymal transition / negative regulation of type I interferon production / protein-lysine-acetyltransferase activity / oogenesis / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / neurogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of autophagy / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / zinc ion binding / nucleoplasm / 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 ...: / 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-NBJ / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHermans, S.J. / Chung, M.C. / Parker, M.W. / Thomas, T. / Baell, J.B.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Acylsulfonohydrazide-Derived Inhibitors of the Lysine Acetyltransferase, KAT6A, as Potent Senescence-Inducing Anti-Cancer Agents.
Authors: Priebbenow, D.L. / Leaver, D.J. / Nguyen, N. / Cleary, B. / Lagiakos, H.R. / Sanchez, J. / Xue, L. / Huang, F. / Sun, Y. / Mujumdar, P. / Mudududdla, R. / Varghese, S. / Teguh, S. / Charman, ...Authors: Priebbenow, D.L. / Leaver, D.J. / Nguyen, N. / Cleary, B. / 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. / Shackleford, D.M. / Katneni, K. / Cuellar, M. / Strasser, J.M. / Dahlin, J.L. / Walters, M.A. / Street, I.P. / Monahan, B.J. / Jarman, K.E. / Jousset Sabroux, H. / Falk, H. / Chung, M.C. / Hermans, S.J. / Downer, N.L. / Parker, M.W. / Voss, A.K. / Thomas, T. / Baell, J.B.
History
DepositionMay 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,8886
Polymers32,1401
Non-polymers7485
Water86548
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)46.560, 57.290, 122.490
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 , 1 types, 1 molecules A

#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 / 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

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Non-polymers , 5 types, 53 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NBJ / N'-[(2-fluorophenyl)sulfonyl]-3-iodobenzohydrazide


Mass: 420.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10FIN2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / 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: Jul 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→122.49 Å / Num. obs: 22844 / % possible obs: 99.91 % / Redundancy: 2 % / CC1/2: 0.998 / Rpim(I) all: 0.03926 / Rrim(I) all: 0.05552 / Net I/σ(I): 12.56
Reflection shellResolution: 2→2.071 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.22 / Num. unique obs: 2228 / Rpim(I) all: 0.2289 / Rrim(I) all: 0.3237 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OIN

6oin


Resolution: 2→27.058 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 1169 5.12 %RANDOM
Rwork0.1914 ---
obs0.1931 22844 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→27.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 38 48 2321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112368
X-RAY DIFFRACTIONf_angle_d1.2323210
X-RAY DIFFRACTIONf_dihedral_angle_d8.1671945
X-RAY DIFFRACTIONf_chiral_restr0.063331
X-RAY DIFFRACTIONf_plane_restr0.008399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.28991430.23042634X-RAY DIFFRACTION100
2.091-2.20120.22031430.20962696X-RAY DIFFRACTION100
2.2012-2.33910.26231390.20442669X-RAY DIFFRACTION100
2.3391-2.51950.24581450.20672672X-RAY DIFFRACTION100
2.5195-2.77290.23481450.2032681X-RAY DIFFRACTION100
2.7729-3.17360.25511520.21062712X-RAY DIFFRACTION100
3.1736-3.99630.21831550.17572734X-RAY DIFFRACTION100
3.9963-27.06090.18661470.17242877X-RAY DIFFRACTION100

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