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- PDB-8e6o: Crystal structure of human GCN5 histone acetyltransferase domain -

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Basic information

Entry
Database: PDB / ID: 8e6o
TitleCrystal structure of human GCN5 histone acetyltransferase domain
ComponentsHistone acetyltransferase KAT2A
KeywordsTRANSFERASE / histone acetyltransferase
Function / homology
Function and homology information


histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / positive regulation of cell projection organization / : / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / positive regulation of cardiac muscle cell differentiation ...histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / positive regulation of cell projection organization / : / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / positive regulation of cardiac muscle cell differentiation / regulation of stem cell population maintenance / regulation of bone development / regulation of regulatory T cell differentiation / negative regulation of centriole replication / transcription factor TFTC complex / telencephalon development / histone H3 acetyltransferase activity / internal peptidyl-lysine acetylation / histone H3K18 acetyltransferase activity / ATAC complex / SAGA complex / Cardiogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / limb development / NOTCH4 Intracellular Domain Regulates Transcription / regulation of T cell activation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of tubulin deacetylation / peptide-lysine-N-acetyltransferase activity / midbrain development / intracellular distribution of mitochondria / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / Formation of paraxial mesoderm / regulation of RNA splicing / RNA Polymerase I Transcription Initiation / regulation of embryonic development / histone acetyltransferase complex / negative regulation of gluconeogenesis / regulation of DNA repair / long-term memory / somitogenesis / histone acetyltransferase activity / positive regulation of gluconeogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / histone acetyltransferase / response to nutrient levels / cellular response to nerve growth factor stimulus / neural tube closure / gluconeogenesis / positive regulation of cytokine production / regulation of synaptic plasticity / multicellular organism growth / regulation of protein stability / B-WICH complex positively regulates rRNA expression / response to organic cyclic compound / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / histone deacetylase binding / cellular response to tumor necrosis factor / heart development / HATs acetylate histones / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsLu, X.T. / Tao, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationC-1565 United States
CitationJournal: To Be Published
Title: Crystal structure of human GCN5 histone acetyltransferase domain
Authors: Lu, X.T. / Tao, Y.J.
History
DepositionAug 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT2A
B: Histone acetyltransferase KAT2A
C: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1356
Polymers57,6163
Non-polymers2,5193
Water2,972165
1
A: Histone acetyltransferase KAT2A
B: Histone acetyltransferase KAT2A
C: Histone acetyltransferase KAT2A
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)481,08248
Polymers460,93124
Non-polymers20,15024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)137.889, 137.889, 154.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-847-

HOH

21B-857-

HOH

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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: 19205.479 Da / Num. of mol.: 3 / Fragment: catalytic domain, UNP residues 497-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2A, GCN5, GCN5L2 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta
References: UniProt: Q92830, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-UQ3 / S-{(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (2R)-2-hydroxypropanethioate / Lactyl-CoA


Mass: 839.597 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H40N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1 M Succinic acid pH 7.0, 0.1 M HEPES pH 7, and 1% w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 30628 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 44.55 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.086 / Χ2: 1.298 / Net I/σ(I): 9.4 / Num. measured all: 385378
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.37-2.4111.40.7715230.8640.2390.8070.842100
2.41-2.45120.69614950.910.210.7280.883100
2.45-2.512.60.57515110.9330.1690.60.894100
2.5-2.5512.90.50115110.9430.1450.5220.925100
2.55-2.6112.90.43215030.9670.1250.450.943100
2.61-2.6712.80.36215070.9740.1050.3770.997100
2.67-2.7412.80.33215010.9750.0970.3460.996100
2.74-2.8112.70.26315180.9820.0770.2751.057100
2.81-2.8912.60.21315320.9880.0620.2221.123100
2.89-2.9912.60.17415010.9930.0510.1811.183100
2.99-3.0912.50.14115180.9950.0410.1471.295100
3.09-3.2212.30.12415290.9950.0370.131.482100
3.22-3.3612.10.10515440.9960.0320.111.776100
3.36-3.54120.08915080.9970.0270.0931.999100
3.54-3.76120.07515420.9970.0230.0791.911100
3.76-4.0512.20.06115370.9980.0180.0641.708100
4.05-4.4612.40.05615480.9990.0160.0581.818100
4.46-5.113.30.05215460.9990.0150.0541.87699.9
5.1-6.4314.30.04415850.9990.0120.0451.29299.9
6.43-5013.20.03166910.0090.0320.99499.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TRL

5trl


Resolution: 2.37→43.6 Å / SU ML: 0.2863 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 1999 6.55 %
Rwork0.2051 28529 -
obs0.2075 30528 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.24 Å2
Refinement stepCycle: LAST / Resolution: 2.37→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 159 165 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254263
X-RAY DIFFRACTIONf_angle_d0.53125772
X-RAY DIFFRACTIONf_chiral_restr0.0455612
X-RAY DIFFRACTIONf_plane_restr0.0032723
X-RAY DIFFRACTIONf_dihedral_angle_d5.4382651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.29691380.25871977X-RAY DIFFRACTION98.33
2.43-2.490.29231420.24852022X-RAY DIFFRACTION99.82
2.49-2.570.28731390.23541993X-RAY DIFFRACTION99.58
2.57-2.650.31741420.23552024X-RAY DIFFRACTION99.77
2.65-2.740.30081410.24652001X-RAY DIFFRACTION99.58
2.74-2.850.30421410.2472020X-RAY DIFFRACTION99.91
2.85-2.980.28141420.23952021X-RAY DIFFRACTION99.91
2.98-3.140.29961420.22242038X-RAY DIFFRACTION99.95
3.14-3.340.24651420.21952028X-RAY DIFFRACTION99.91
3.34-3.590.21281430.2022051X-RAY DIFFRACTION100
3.6-3.960.22391440.18482045X-RAY DIFFRACTION100
3.96-4.530.20021460.16692072X-RAY DIFFRACTION99.82
4.53-5.70.22591450.17962088X-RAY DIFFRACTION99.73
5.7-43.60.22191520.20972149X-RAY DIFFRACTION97.58

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