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- PDB-5h86: Human Gcn5 bound to butyryl-CoA -

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Basic information

Entry
Database: PDB / ID: 5h86
TitleHuman Gcn5 bound to butyryl-CoA
ComponentsHistone acetyltransferase KAT2A
KeywordsTRANSFERASE / Gcn5 / Coenzyme A
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) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase ...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) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Butyryl Coenzyme A / Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsWolberger, C. / Ringel, A.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098522 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural basis for acyl-group discrimination by human Gcn5L2.
Authors: Ringel, A.E. / Wolberger, C.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3063
Polymers19,4071
Non-polymers9002
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.246, 38.246, 186.965
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Histone acetyltransferase KAT2A / General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / HsGCN5 ...General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / HsGCN5 / Lysine acetyltransferase 2A / STAF97


Mass: 19406.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2A, GCN5, GCN5L2, HGCN5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92830, histone acetyltransferase
#2: Chemical ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)


Mass: 837.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O17P3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 10% (v/v) 2-propanol, 3% glycerol, 100 mM HEPES, pH 7.8, and 11% (w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.08→24.81 Å / Num. obs: 9086 / % possible obs: 98.06 % / Redundancy: 6.4 % / Net I/σ(I): 16.86
Reflection shellResolution: 2.08→2.154 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.1861 / Mean I/σ(I) obs: 5.39 / % possible all: 87.88

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z4R

1z4r


Resolution: 2.08→24.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.116 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19421 435 4.8 %RANDOM
Rwork0.15642 ---
obs0.15823 8650 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.113 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.26 Å20 Å2
2--0.26 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.08→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 57 88 1479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191455
X-RAY DIFFRACTIONr_bond_other_d0.0010.021384
X-RAY DIFFRACTIONr_angle_refined_deg1.2532.0021972
X-RAY DIFFRACTIONr_angle_other_deg0.91333181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6195168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93423.06562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31315239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.445157
X-RAY DIFFRACTIONr_chiral_restr0.1990.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 34 -
Rwork0.197 579 -
obs--85.85 %

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