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- PDB-6j3p: Crystal structure of the human GCN5 bromodomain in complex with c... -

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Basic information

Entry
Database: PDB / ID: 6j3p
TitleCrystal structure of the human GCN5 bromodomain in complex with compound (R,R)-36n
ComponentsHistone acetyltransferase KAT2A
KeywordsTRANSFERASE / Crystal structure of the human GCN5 bromodomain in complex with compound (R / R)-36n
Function / homology
Function and homology information


histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / positive regulation of cell projection organization / regulation of cartilage development / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation ...histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / positive regulation of cell projection organization / regulation of cartilage development / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation / regulation of bone development / negative regulation of centriole replication / regulation of regulatory T cell differentiation / telencephalon development / transcription factor TFTC complex / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / histone H3K18 acetyltransferase activity / ATAC complex / limb development / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Cardiogenesis / regulation of T cell activation / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / midbrain development / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / intracellular distribution of mitochondria / Formation of paraxial mesoderm / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of RNA splicing / regulation of embryonic development / histone acetyltransferase complex / negative regulation of gluconeogenesis / long-term memory / somitogenesis / regulation of DNA repair / histone acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to nutrient levels / cellular response to nerve growth factor stimulus / positive regulation of cytokine production / gluconeogenesis / neural tube closure / regulation of protein stability / B-WICH complex positively regulates rRNA expression / regulation of synaptic plasticity / multicellular organism growth / response to organic cyclic compound / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / 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-like / Histone Acetyltransferase; Chain A ...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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B8O / Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsHuang, L.Y. / Li, H. / Niu, L. / Wu, C.Y. / Yu, Y.M. / Li, L.L. / Yang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81473140, 81573349, 81773633, and 21772130 China
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Pyrrolo[3,2- d]pyrimidin-4-one Derivatives as a New Class of Potent and Cell-Active Inhibitors of P300/CBP-Associated Factor Bromodomain.
Authors: Huang, L. / Li, H. / Li, L. / Niu, L. / Seupel, R. / Wu, C. / Cheng, W. / Chen, C. / Ding, B. / Brennan, P.E. / Yang, S.
History
DepositionJan 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,7944
Polymers32,0032
Non-polymers7912
Water5,152286
1
A: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3972
Polymers16,0011
Non-polymers3951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3972
Polymers16,0011
Non-polymers3951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.572, 73.092, 76.222
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 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 succinyltransferase KAT2A / Lysine acetyltransferase 2A / STAF97


Mass: 16001.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2A, GCN5, GCN5L2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92830, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-B8O / 2-{[(3R,5R)-5-(2,3-dihydro-1,4-benzodioxin-6-yl)-1-methylpiperidin-3-yl]amino}-3-methyl-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one


Mass: 395.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.598→50 Å / Num. obs: 34345 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 30.167
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 34345 / Rsym value: 0.463

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3199)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mlj

5mlj


Resolution: 1.598→39.114 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.23
RfactorNum. reflection% reflection
Rfree0.1811 1991 5.81 %
Rwork0.1545 --
obs0.1561 34284 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.598→39.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 58 286 2107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171900
X-RAY DIFFRACTIONf_angle_d1.4682579
X-RAY DIFFRACTIONf_dihedral_angle_d15.771139
X-RAY DIFFRACTIONf_chiral_restr0.08264
X-RAY DIFFRACTIONf_plane_restr0.011323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5982-1.63820.19941260.15982154X-RAY DIFFRACTION95
1.6382-1.68250.18111400.14532295X-RAY DIFFRACTION100
1.6825-1.7320.18081450.14572254X-RAY DIFFRACTION100
1.732-1.78790.1831410.14292273X-RAY DIFFRACTION100
1.7879-1.85180.17821390.14912291X-RAY DIFFRACTION100
1.8518-1.92590.19211380.15262295X-RAY DIFFRACTION100
1.9259-2.01360.17371440.14522307X-RAY DIFFRACTION100
2.0136-2.11970.16081460.14892286X-RAY DIFFRACTION100
2.1197-2.25250.16751390.14232313X-RAY DIFFRACTION100
2.2525-2.42640.18551440.13972306X-RAY DIFFRACTION100
2.4264-2.67050.2031380.15652331X-RAY DIFFRACTION100
2.6705-3.05680.16111530.15482342X-RAY DIFFRACTION100
3.0568-3.85080.17731440.15732367X-RAY DIFFRACTION100
3.8508-39.12580.19811540.17512479X-RAY DIFFRACTION100

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