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- PDB-6ba2: Crystal structure of MYST acetyltransferase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6ba2
TitleCrystal structure of MYST acetyltransferase domain in complex with inhibitor
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE / acetyltransferase / inhibitor / complex / MYST
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-7KM / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85003821102 Å
AuthorsHermans, S.J. / Chung, M.C. / Peat, T.S. / Baell, J.B. / Thomas, T. / Parker, M.W.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1030704 Australia
National Health and Medical Research Council (NHMRC, Australia)1080146 Australia
CitationJournal: Nature / Year: 2018
Title: Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumour growth.
Authors: Baell, J.B. / Leaver, D.J. / Hermans, S.J. / Kelly, G.L. / Brennan, M.S. / Downer, N.L. / Nguyen, N. / Wichmann, J. / McRae, H.M. / Yang, Y. / Cleary, B. / Lagiakos, H.R. / Mieruszynski, S. ...Authors: Baell, J.B. / Leaver, D.J. / Hermans, S.J. / Kelly, G.L. / Brennan, M.S. / Downer, N.L. / Nguyen, N. / Wichmann, J. / McRae, H.M. / Yang, Y. / Cleary, B. / Lagiakos, H.R. / Mieruszynski, S. / Pacini, G. / Vanyai, H.K. / Bergamasco, M.I. / May, R.E. / Davey, B.K. / Morgan, K.J. / Sealey, A.J. / Wang, B. / Zamudio, N. / Wilcox, S. / Garnham, A.L. / Sheikh, B.N. / Aubrey, B.J. / Doggett, K. / Chung, M.C. / de Silva, M. / Bentley, J. / Pilling, P. / Hattarki, M. / Dolezal, O. / Dennis, M.L. / Falk, H. / Ren, B. / Charman, S.A. / White, K.L. / Rautela, J. / Newbold, A. / Hawkins, E.D. / Johnstone, R.W. / Huntington, N.D. / Peat, T.S. / Heath, J.K. / Strasser, A. / Parker, M.W. / Smyth, G.K. / Street, I.P. / Monahan, B.J. / Voss, A.K. / Thomas, T.
History
DepositionOct 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)35,40210
Polymers34,4341
Non-polymers9699
Water2,576143
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)46.231, 56.916, 120.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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: 34433.598 Da / Num. of mol.: 1
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 , 6 types, 152 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-7KM / 4-fluoro-5-methyl-N'-(phenylsulfonyl)[1,1'-biphenyl]-3-carbohydrazide


Mass: 384.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2 M NaCl, 0.1 M Tris pH 7.0, 0.22 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→46.23 Å / Num. obs: 27815 / % possible obs: 99.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 23.5272687774 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.035 / Rrim(I) all: 0.08 / Net I/σ(I): 13.4
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 5 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1669 / CC1/2: 0.741 / Rpim(I) all: 0.338 / Rrim(I) all: 0.779 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1496refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MOF Catalytic Domain

Resolution: 1.85003821102→43.186116656 Å / SU ML: 0.195236071411 / Cross valid method: FREE R-VALUE / σ(F): 1.337647998 / Phase error: 23.9887208829
RfactorNum. reflection% reflection
Rfree0.228016935366 1389 5.00144029958 %
Rwork0.193825526814 --
obs0.195614080285 27772 99.0936987083 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.4680609733 Å2
Refinement stepCycle: LAST / Resolution: 1.85003821102→43.186116656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 60 143 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01491150716942280
X-RAY DIFFRACTIONf_angle_d1.104908175473081
X-RAY DIFFRACTIONf_chiral_restr0.0607253072838319
X-RAY DIFFRACTIONf_plane_restr0.00687600654423382
X-RAY DIFFRACTIONf_dihedral_angle_d12.77613555471339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.91620.2929721625451210.2468014357382582X-RAY DIFFRACTION98.3982526392
1.9162-1.99290.2660617627611210.2271079088592595X-RAY DIFFRACTION98.7636363636
1.9929-2.08360.26809984031330.2127281578222600X-RAY DIFFRACTION98.9142236699
2.0836-2.19340.2648229946951280.1982277473672619X-RAY DIFFRACTION99.1696750903
2.1934-2.33080.2217895093281270.1952851875552612X-RAY DIFFRACTION99.2391304348
2.3308-2.51080.2556465658231260.1987591776742627X-RAY DIFFRACTION99.4221740701
2.5108-2.76340.2577198473291510.2086865886562645X-RAY DIFFRACTION99.6081225508
2.7634-3.16320.2221914699681710.1924613982462643X-RAY DIFFRACTION99.7518610422
3.1632-3.98480.1877639116551520.1740945920392680X-RAY DIFFRACTION99.8941798942
3.9848-43.19790.2190935238311590.1852860513852780X-RAY DIFFRACTION97.9013990673

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