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- PDB-1pu9: Crystal Structure of Tetrahymena GCN5 with Bound Coenzyme A and a... -

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Basic information

Entry
Database: PDB / ID: 1pu9
TitleCrystal Structure of Tetrahymena GCN5 with Bound Coenzyme A and a 19-residue Histone H3 Peptide
Components
  • HAT A1
  • Histone H3
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / HISTONE ACETYLTRANSFERASE / GCN5-RELATED N-ACETYLTRANSFERASE / COA-BINDING PROTEIN / TERNARY COMPLEX / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


chromatin organization => GO:0006325 / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / replication fork protection complex ...chromatin organization => GO:0006325 / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / replication fork protection complex / histone H3 acetyltransferase activity / Oxidative Stress Induced Senescence / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / histone acetyltransferase complex / intracellular copper ion homeostasis / histone acetyltransferase / CENP-A containing nucleosome / aerobic respiration / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Histone H3 / Histone H3 / histone acetyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsClements, A. / Poux, A.N. / Lo, W.S. / Pillus, L. / Berger, S.L. / Marmorstein, R.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural basis for histone and phospho-histone binding by the GCN5 histone acetyltransferase
Authors: Clements, A. / Poux, A.N. / Lo, W.S. / Pillus, L. / Berger, S.L. / Marmorstein, R.
History
DepositionJun 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The author state: " This construct was cloned directly from the Tetrahymena thermophilia ...SEQUENCE The author state: " This construct was cloned directly from the Tetrahymena thermophilia genome. It is assumed that the protein sequence is correct, particularly in the case of the phenylalanine, as it is highly conserved among Gcn5 histone acetyltransferases from other species."

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAT A1
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2453
Polymers21,4772
Non-polymers7681
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-4 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.730, 64.730, 96.416
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HAT A1


Mass: 19457.658 Da / Num. of mol.: 1 / Fragment: residues 48-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Plasmid: PRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q27198
#2: Protein/peptide Histone H3


Mass: 2019.352 Da / Num. of mol.: 1 / Fragment: Residues 305-323 / Source method: obtained synthetically
Details: This protein naturally occurs in Saccharomyces cerevisiae (Baker's yeast).
References: UniProt: P02303, UniProt: P61830*PLUS
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Ammonium sulfate, MnCl2, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.4 mMtGCN51drop
21.0 mMCoA1drop
31.5 mMH3-derived peptide1drop
41.6 Mammonium sulfate1reservoir
510-50 mM1reservoirMnCl2
650 mMTris1reservoirpH7.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9213
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9213 Å / Relative weight: 1
ReflectionResolution: 2.24→27 Å / Num. obs: 10007 / % possible obs: 96 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.4 Å2
Reflection shellResolution: 2.24→2.39 Å
Reflection
*PLUS
Highest resolution: 2.21 Å / Lowest resolution: 50 Å / Num. obs: 22051 / % possible obs: 99.5 % / Num. measured all: 67990 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
Highest resolution: 2.21 Å / Lowest resolution: 2.35 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QSN

1qsn


Resolution: 2.3→21.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1492487.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1010 10.1 %RANDOM
Rwork0.236 ---
obs0.236 10007 92.3 %-
all-10843 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.19 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å24.78 Å20 Å2
2--4.23 Å20 Å2
3----8.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→21.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 48 106 1631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 178 10.6 %
Rwork0.261 1502 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3COA_OLD.PARCOA_OLD.TOP
X-RAY DIFFRACTION4
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.64
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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