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- PDB-8h6d: Crystal structure of human GCN5 histone acetyltransferase domain ... -

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Basic information

Entry
Database: PDB / ID: 8h6d
TitleCrystal structure of human GCN5 histone acetyltransferase domain bound with glutaryl-CoA
ComponentsHistone acetyltransferase KAT2A
KeywordsTRANSFERASE / Complex
Function / homology
Function and homology information


histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / regulation of bone development / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation ...histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / regulation of bone development / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation / negative regulation of centriole replication / positive regulation of cell projection organization / transcription factor TFTC complex / regulation of regulatory T cell differentiation / telencephalon development / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / histone H3K18 acetyltransferase activity / ATAC complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / limb development / Cardiogenesis / regulation of T cell activation / NOTCH4 Intracellular Domain Regulates Transcription / SAGA complex / NOTCH3 Intracellular Domain Regulates Transcription / protein-lysine-acetyltransferase activity / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / Formation of paraxial mesoderm / midbrain development / regulation of RNA splicing / intracellular distribution of mitochondria / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of embryonic development / histone acetyltransferase complex / negative regulation of gluconeogenesis / long-term memory / somitogenesis / histone acetyltransferase activity / regulation of DNA repair / histone acetyltransferase / positive regulation of gluconeogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of cytokine production / gluconeogenesis / neural tube closure / response to nutrient levels / cellular response to nerve growth factor stimulus / regulation of synaptic plasticity / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / B-WICH complex positively regulates rRNA expression / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / multicellular organism growth / histone deacetylase binding / mitotic spindle / cellular response to tumor necrosis factor / HATs acetylate histones / heart development / fibroblast proliferation / protein phosphatase binding / DNA-binding transcription factor binding / in utero embryonic development / transcription coactivator activity / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain, conserved site / Bromodomain signature. ...PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
glutaryl-coenzyme A / Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsLi, N. / Tao, Y.J. / Guo, Y.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch Foundation United States
CitationJournal: Res / Year: 2023
Title: Molecular Basis of KAT2A Selecting Acyl-CoA Cofactors for Histone Modifications.
Authors: Li, S. / Li, N. / He, J. / Zhou, R. / Lu, Z. / Tao, Y.J. / Guo, Y.R. / Wang, Y.
History
DepositionOct 16, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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
C: Histone acetyltransferase KAT2A
D: Histone acetyltransferase KAT2A
E: Histone acetyltransferase KAT2A
F: Histone acetyltransferase KAT2A
B: Histone acetyltransferase KAT2A
A: Histone acetyltransferase KAT2A
G: Histone acetyltransferase KAT2A
H: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,15316
Polymers154,1008
Non-polymers7,0538
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation, Gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.265, 175.265, 175.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein
Histone acetyltransferase KAT2A / General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / hGCN5 / ...General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / hGCN5 / Histone glutaryltransferase KAT2A / Histone succinyltransferase KAT2A / Lysine acetyltransferase 2A / STAF97


Mass: 19262.529 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2A, GCN5, GCN5L2 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q92830, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-GRA / glutaryl-coenzyme A


Mass: 881.633 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C26H42N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.3M Ammonium sulfate, 0.4M Lithium chloride

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 28347 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 58.24 Å2 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.067 / Rrim(I) all: 0.187 / Χ2: 0.932 / Net I/σ(I): 4 / Num. measured all: 213058
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.317.60.61313940.8520.2380.6590.653100
3.31-3.377.60.49914020.8840.1930.5360.693100
3.37-3.437.60.44614160.9050.1730.4790.695100
3.43-3.57.60.39614040.9260.1530.4250.698100
3.5-3.587.60.35113800.9420.1350.3770.728100
3.58-3.667.60.30114110.9470.1170.3230.764100
3.66-3.757.60.25914020.9620.10.2780.79100
3.75-3.857.60.2313940.9690.0890.2470.825100
3.85-3.977.60.20614220.9740.0790.2210.856100
3.97-4.097.60.17913980.980.0690.1920.913100
4.09-4.247.60.16613900.9840.0640.1780.971100
4.24-4.417.60.14714340.9850.0560.1581.033100
4.41-4.617.50.1414170.9880.0540.1511.198100
4.61-4.857.60.14214180.9790.0550.1531.36100
4.85-5.167.50.15314130.9830.0590.1641.333100
5.16-5.567.50.16914040.980.0650.1821.342100
5.56-6.117.50.18314470.9790.0710.1971.178100
6.11-77.40.13514440.9920.0520.1451.013100
7-8.817.30.07514470.9970.0290.0810.83100
8.81-506.90.05215100.9970.020.0560.76299.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TRM

5trm


Resolution: 3.26→48.61 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 1322 4.7 %
Rwork0.1764 26779 -
obs0.1792 28101 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.13 Å2 / Biso mean: 47.0124 Å2 / Biso min: 17.72 Å2
Refinement stepCycle: final / Resolution: 3.26→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10634 0 448 0 11082
Biso mean--59.62 --
Num. residues----1296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.26-3.390.27921490.21222904305399
3.39-3.540.27591610.18362935309699
3.54-3.730.26221440.18422941308599
3.73-3.960.26261380.17929603098100
3.96-4.270.20851500.16282965311599
4.27-4.70.21311520.151629893141100
4.7-5.370.2151700.15852954312499
5.38-6.760.27821030.21913050315399
6.77-48.610.20731550.17093081323699

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