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- PDB-6ct2: MYST histone acetyltransferase KAT6A/B in complex with WM-1119 -

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Basic information

Entry
Database: PDB / ID: 6ct2
TitleMYST histone acetyltransferase KAT6A/B in complex with WM-1119
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE/INHIBITOR / complex / lysine acetyltransferases / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation / post-embryonic hemopoiesis / NSL complex / negative regulation of epithelial to mesenchymal transition / peptide-lysine-N-acetyltransferase activity / negative regulation of type I interferon production / oogenesis / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / transcription initiation-coupled chromatin remodeling / regulation of autophagy / transcription coregulator activity / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / nucleoplasm / nucleus / metal ion binding
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-FCV / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.128 Å
AuthorsRen, B. / Peat, T.S.
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
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation_author
Revision 1.2Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0124
Polymers34,5331
Non-polymers4793
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.892, 56.080, 120.919
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: 34532.727 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
#2: Chemical ChemComp-FCV / 3-fluoro-N'-[(2-fluorophenyl)sulfonyl]-5-(pyridin-2-yl)benzohydrazide


Mass: 389.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13F2N3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 0.196 M MgCl2, 19.5 % PEG 3350, and 0.1 M bis-tris chloride at pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.128→45.89 Å / Num. obs: 18176 / % possible obs: 99.7 % / Redundancy: 7.1 % / Net I/σ(I): 8.5
Reflection shellResolution: 2.13→2.19 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.128→42.906 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8
RfactorNum. reflection% reflection
Rfree0.2355 1812 10 %
Rwork0.2005 --
obs0.2041 18122 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.128→42.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 29 135 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032387
X-RAY DIFFRACTIONf_angle_d0.653245
X-RAY DIFFRACTIONf_dihedral_angle_d3.6021972
X-RAY DIFFRACTIONf_chiral_restr0.048338
X-RAY DIFFRACTIONf_plane_restr0.005405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1276-2.18510.28751330.27021192X-RAY DIFFRACTION96
2.1851-2.24940.27221360.23941219X-RAY DIFFRACTION100
2.2494-2.3220.26211360.23131234X-RAY DIFFRACTION100
2.322-2.4050.24251370.22781227X-RAY DIFFRACTION100
2.405-2.50130.26121380.23061243X-RAY DIFFRACTION100
2.5013-2.61510.24351380.22571252X-RAY DIFFRACTION100
2.6151-2.7530.2831380.22261246X-RAY DIFFRACTION100
2.753-2.92540.22791380.21751237X-RAY DIFFRACTION100
2.9254-3.15120.28781400.20511268X-RAY DIFFRACTION100
3.1512-3.46820.22071410.18861261X-RAY DIFFRACTION100
3.4682-3.96980.2391400.16991262X-RAY DIFFRACTION100
3.9698-5.00030.17641440.16371299X-RAY DIFFRACTION100
5.0003-42.91450.22721530.20311370X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3045-0.1440.64251.2581-0.84263.11880.0717-0.0421-0.1770.2451-0.02230.00410.15380.2571-0.02960.25130.01110.01450.2825-0.01470.207614.9428-17.073-3.1635
23.3637-1.14612.51531.2749-1.62245.5717-0.058-0.2421-0.0855-0.03220.1152-0.04490.08340.10630.02490.2435-0.0304-0.01560.217-0.00450.226224.5417-7.7055-6.3084
33.06470.4780.82751.7058-0.43934.0094-0.0710.1101-0.0798-0.122-0.0215-0.08070.26790.22190.06730.1965-0.00850.00380.1830.00580.163417.5128-12.6436-20.0861
43.27890.01231.16921.9983-0.31474.1358-0.0678-0.09040.2539-0.31250.19490.23240.1339-0.1767-0.00210.2373-0.0279-0.03870.1572-0.03250.26133.2383-13.2878-29.5167
53.27792.43240.77332.12431.39022.2251-0.44980.45760.4229-0.45470.25150.4027-0.1632-0.07370.14260.4208-0.0256-0.06730.28910.02340.3271-3.2675-15.852-40.9613
62.23972.25780.65632.38720.52950.30810.1419-0.73140.62930.0024-0.32870.81280.2053-0.22130.15610.43420.037-0.02460.43980.02790.48553.6746-2.3778-30.2591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 506 through 528 )
2X-RAY DIFFRACTION2chain 'A' and (resid 529 through 575 )
3X-RAY DIFFRACTION3chain 'A' and (resid 576 through 672 )
4X-RAY DIFFRACTION4chain 'A' and (resid 673 through 705 )
5X-RAY DIFFRACTION5chain 'A' and (resid 706 through 748 )
6X-RAY DIFFRACTION6chain 'A' and (resid 749 through 779 )

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