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- PDB-7y43: Crystal structure of the KAT6A WH domain and its bound double str... -

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Basic information

Entry
Database: PDB / ID: 7y43
TitleCrystal structure of the KAT6A WH domain and its bound double stranded DNA
Components
  • DNA (5'-D(*GP*GP*AP*GP*TP*GP*CP*GP*CP*AP*CP*TP*CP*C)-3')
  • Histone acetyltransferase KAT6A
KeywordsDNA BINDING PROTEIN/DNA / CpG islands / Winged-helix domain / acetyltransferase / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex ...histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / protein acetylation / acetyltransferase activity / chromosome organization / histone acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / regulation of signal transduction by p53 class mediator / transcription coregulator activity / PML body / cellular senescence / nucleosome / nucleosome assembly / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. ...: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWang, Z. / Jia, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071204 China
National Natural Science Foundation of China (NSFC)31870725 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain.
Authors: Weber, L.M. / Jia, Y. / Stielow, B. / Gisselbrecht, S.S. / Cao, Y. / Ren, Y. / Rohner, I. / King, J. / Rothman, E. / Fischer, S. / Simon, C. / Forne, I. / Nist, A. / Stiewe, T. / Bulyk, M.L. ...Authors: Weber, L.M. / Jia, Y. / Stielow, B. / Gisselbrecht, S.S. / Cao, Y. / Ren, Y. / Rohner, I. / King, J. / Rothman, E. / Fischer, S. / Simon, C. / Forne, I. / Nist, A. / Stiewe, T. / Bulyk, M.L. / Wang, Z. / Liefke, R.
History
DepositionJun 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase KAT6A
B: DNA (5'-D(*GP*GP*AP*GP*TP*GP*CP*GP*CP*AP*CP*TP*CP*C)-3')
C: DNA (5'-D(*GP*GP*AP*GP*TP*GP*CP*GP*CP*AP*CP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2474
Polymers18,2233
Non-polymers241
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-19 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.479, 46.479, 153.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21B-109-

HOH

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Components

#1: Protein Histone acetyltransferase KAT6A / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt- ...MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt-related transcription factor-binding protein 2 / Zinc finger protein 220


Mass: 9659.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT6A / Production host: Escherichia coli (E. coli) / References: UniProt: Q92794, histone acetyltransferase
#2: DNA chain DNA (5'-D(*GP*GP*AP*GP*TP*GP*CP*GP*CP*AP*CP*TP*CP*C)-3')


Mass: 4281.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium acetate tetrahydrate, 20% polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 28018 / % possible obs: 100 % / Redundancy: 24.7 % / Biso Wilson estimate: 22.67 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 41.7
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.29 / Num. unique obs: 1352

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LUI

6lui


Resolution: 1.5→20.6 Å / SU ML: 0.1861 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7507
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 1345 4.82 %
Rwork0.2269 26535 -
obs0.2274 27880 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms624 568 1 138 1331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641268
X-RAY DIFFRACTIONf_angle_d0.88371827
X-RAY DIFFRACTIONf_chiral_restr0.0476207
X-RAY DIFFRACTIONf_plane_restr0.0051136
X-RAY DIFFRACTIONf_dihedral_angle_d26.0966525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.27211270.26752588X-RAY DIFFRACTION99.78
1.55-1.620.2761260.24882595X-RAY DIFFRACTION100
1.62-1.690.30271240.25272592X-RAY DIFFRACTION99.45
1.69-1.780.31491220.27562626X-RAY DIFFRACTION100
1.78-1.890.29181210.25972632X-RAY DIFFRACTION100
1.89-2.040.24441330.24032644X-RAY DIFFRACTION100
2.04-2.240.27021350.22442629X-RAY DIFFRACTION100
2.24-2.560.21931420.23632673X-RAY DIFFRACTION100
2.57-3.230.27281510.23762695X-RAY DIFFRACTION99.93
3.23-20.60.19221640.2012861X-RAY DIFFRACTION99.31

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