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- PDB-8h7a: Crystal structure of the dimer form KAT6A WH domain with its boun... -

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Basic information

Entry
Database: PDB / ID: 8h7a
TitleCrystal structure of the dimer form KAT6A WH domain with its bound double stranded DNA
Components
  • DNA (5'-D(*GP*GP*TP*CP*CP*GP*AP*CP*GP*GP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*CP*CP*GP*TP*CP*GP*GP*AP*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: 1.92 Å
AuthorsWang, Z. / Cao, 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
DepositionOct 19, 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: Histone acetyltransferase KAT6A
C: DNA (5'-D(*GP*GP*TP*CP*CP*GP*AP*CP*GP*GP*AP*CP*C)-3')
D: DNA (5'-D(*GP*GP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*C)-3')
E: Histone acetyltransferase KAT6A
F: Histone acetyltransferase KAT6A
G: DNA (5'-D(*GP*GP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*CP*CP*GP*AP*CP*GP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,62612
Polymers54,5298
Non-polymers974
Water4,630257
1
A: Histone acetyltransferase KAT6A
B: Histone acetyltransferase KAT6A
C: DNA (5'-D(*GP*GP*TP*CP*CP*GP*AP*CP*GP*GP*AP*CP*C)-3')
D: DNA (5'-D(*GP*GP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3136
Polymers27,2654
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-17 kcal/mol
Surface area12410 Å2
MethodPISA
2
E: Histone acetyltransferase KAT6A
F: Histone acetyltransferase KAT6A
G: DNA (5'-D(*GP*GP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*CP*CP*GP*AP*CP*GP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3136
Polymers27,2654
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-17 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.007, 40.060, 81.252
Angle α, β, γ (deg.)90.116, 89.989, 113.880
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Histone acetyltransferase KAT6A


Mass: 9659.217 Da / Num. of mol.: 4
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*TP*CP*CP*GP*AP*CP*GP*GP*AP*CP*C)-3')


Mass: 3977.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*GP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*C)-3')


Mass: 3968.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Magnesium chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.1 M HEPES sodium pH 7.0, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 33965 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.54 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 20.97
Reflection shellResolution: 1.93→1.96 Å / Rmerge(I) obs: 0.399 / Num. unique obs: 1640

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y43

7y43


Resolution: 1.92→27.23 Å / SU ML: 0.2718 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.2574 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2346 1583 4.67 %
Rwork0.195 32333 -
obs0.1969 33916 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.36 Å2
Refinement stepCycle: LAST / Resolution: 1.92→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 1054 4 257 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813651
X-RAY DIFFRACTIONf_angle_d0.95585136
X-RAY DIFFRACTIONf_chiral_restr0.0491585
X-RAY DIFFRACTIONf_plane_restr0.0059474
X-RAY DIFFRACTIONf_dihedral_angle_d26.02421490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.990.37981550.27182719X-RAY DIFFRACTION89.98
1.99-2.060.29951550.22392864X-RAY DIFFRACTION97.2
2.06-2.140.25291300.21042975X-RAY DIFFRACTION97.52
2.14-2.240.25421530.21632992X-RAY DIFFRACTION97.22
2.24-2.350.30481020.21092978X-RAY DIFFRACTION97.59
2.35-2.50.26911140.21093028X-RAY DIFFRACTION97.67
2.5-2.690.24741750.22662903X-RAY DIFFRACTION97.62
2.69-2.970.27341360.22822950X-RAY DIFFRACTION97.53
2.97-3.390.24411780.20882953X-RAY DIFFRACTION98.06
3.39-4.270.20361450.16942995X-RAY DIFFRACTION98.43
4.27-27.230.18561400.1652976X-RAY DIFFRACTION97.83

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