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- PDB-1z4r: Human GCN5 Acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 1z4r
TitleHuman GCN5 Acetyltransferase
ComponentsGeneral control of amino acid synthesis protein 5-like 2
KeywordsTRANSFERASE / GCN5 / Acetyltransferase / SGC / Structural Genomics / Structural Genomics Consortium
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
ACETYL COENZYME *A / Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsDong, A. / Bernstein, G. / Schuetz, A. / Antoshenko, T. / Wu, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Dong, A. / Bernstein, G. / Schuetz, A. / Antoshenko, T. / Wu, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Plotnikov, A. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of a binary complex between human GCN5 histone acetyltransferase domain and acetyl coenzyme A
Authors: Schuetz, A. / Bernstein, G. / Dong, A. / Antoshenko, T. / Wu, H. / Loppnau, P. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionMar 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General control of amino acid synthesis protein 5-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2162
Polymers19,4071
Non-polymers8101
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.090, 38.090, 186.340
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 General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / hsGCN5 / STAF97


Mass: 19406.660 Da / Num. of mol.: 1 / Fragment: Residues 497-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCN5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92830, histone acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7
Details: 15% (v/v) ethanol, 100 mM Tris, pH 7.0, VAPOR DIFFUSION, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 8, 2005 / Details: VeriMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→32.98 Å / Num. obs: 15315 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.71 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 19.7
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 1.73 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1792 / Rsym value: 0.169 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YGH

1ygh


Resolution: 1.74→32.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 762661.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 592 4 %RANDOM
Rwork0.197 ---
all0.197 ---
obs0.197 14729 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6544 Å2 / ksol: 0.3745 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å22.58 Å20 Å2
2--3.09 Å20 Å2
3----6.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.74→32.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 51 131 1512
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 1.74→1.85 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 86 4.7 %
Rwork0.275 1750 -
obs--71.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3COA_XPLOR_PAR.TXTCOA_XPLOR_TOP.TXT

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