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- PDB-3to7: Crystal structure of yeast Esa1 HAT domain bound to coenzyme A wi... -

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Basic information

Entry
Database: PDB / ID: 3to7
TitleCrystal structure of yeast Esa1 HAT domain bound to coenzyme A with active site lysine acetylated
ComponentsHistone acetyltransferase ESA1
KeywordsTRANSFERASE / MYST family / histone acetyltransferase
Function / homology
Function and homology information


DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / histone H4 acetyltransferase activity / rDNA heterochromatin formation ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / histone H4 acetyltransferase activity / rDNA heterochromatin formation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptide N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / NuA4 histone acetyltransferase complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / nucleosome / regulation of cell cycle / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
N-acetyl transferase-like / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain ...N-acetyl transferase-like / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CACODYLIC ACID / COENZYME A / Histone acetyltransferase ESA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYuan, H. / Ding, E.C. / Marmorstein, R.
CitationJournal: Embo J. / Year: 2011
Title: MYST protein acetyltransferase activity requires active site lysine autoacetylation.
Authors: Yuan, H. / Rossetto, D. / Mellert, H. / Dang, W. / Srinivasan, M. / Johnson, J. / Hodawadekar, S. / Ding, E.C. / Speicher, K. / Abshiru, N. / Perry, R. / Wu, J. / Yang, C. / Zheng, Y.G. / ...Authors: Yuan, H. / Rossetto, D. / Mellert, H. / Dang, W. / Srinivasan, M. / Johnson, J. / Hodawadekar, S. / Ding, E.C. / Speicher, K. / Abshiru, N. / Perry, R. / Wu, J. / Yang, C. / Zheng, Y.G. / Speicher, D.W. / Thibault, P. / Verreault, A. / Johnson, F.B. / Berger, S.L. / Sternglanz, R. / McMahon, S.B. / Cote, J. / Marmorstein, R.
History
DepositionSep 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase ESA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3396
Polymers33,1531
Non-polymers1,1865
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone acetyltransferase ESA1
hetero molecules

A: Histone acetyltransferase ESA1
hetero molecules

A: Histone acetyltransferase ESA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,01718
Polymers99,4593
Non-polymers3,55715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12160 Å2
ΔGint-42 kcal/mol
Surface area40570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.040, 183.040, 183.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone acetyltransferase ESA1


Mass: 33153.070 Da / Num. of mol.: 1 / Fragment: UNP residues 160-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ESA1, YOR244W, O5257 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08649, histone acetyltransferase

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Non-polymers , 5 types, 198 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.85 Å3/Da / Density % sol: 68.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 1.6 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2011 / Details: TOROIDAL FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 41363 / Num. obs: 41363 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 27.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2045 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MJA

1mja


Resolution: 1.9→30.507 Å / SU ML: 0.22 / σ(F): 0.03 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2066 5.03 %RANDOM
Rwork0.1978 ---
obs0.1992 41059 99.64 %-
all-41059 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 19.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 68 193 2598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082495
X-RAY DIFFRACTIONf_angle_d1.0933380
X-RAY DIFFRACTIONf_dihedral_angle_d15.439956
X-RAY DIFFRACTIONf_chiral_restr0.079353
X-RAY DIFFRACTIONf_plane_restr0.004416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94430.32651340.26452548X-RAY DIFFRACTION100
1.9443-1.99290.24961120.21982590X-RAY DIFFRACTION100
1.9929-2.04680.24131520.19392524X-RAY DIFFRACTION100
2.0468-2.1070.22771310.1812575X-RAY DIFFRACTION100
2.107-2.1750.23051320.18622566X-RAY DIFFRACTION100
2.175-2.25270.19611300.18572581X-RAY DIFFRACTION100
2.2527-2.34280.24661630.1942549X-RAY DIFFRACTION100
2.3428-2.44940.22341260.20792594X-RAY DIFFRACTION100
2.4494-2.57850.24381140.21352599X-RAY DIFFRACTION100
2.5785-2.73990.22391520.21762562X-RAY DIFFRACTION99
2.7399-2.95130.26531340.22712615X-RAY DIFFRACTION100
2.9513-3.2480.22771490.20992602X-RAY DIFFRACTION100
3.248-3.71730.20661510.18452621X-RAY DIFFRACTION100
3.7173-4.68070.18181370.15822671X-RAY DIFFRACTION100
4.6807-30.51060.23681490.20992796X-RAY DIFFRACTION100

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