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- PDB-3to6: Crystal structure of yeast Esa1 HAT domain complexed with H4K16Co... -

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Basic information

Entry
Database: PDB / ID: 3to6
TitleCrystal structure of yeast Esa1 HAT domain complexed with H4K16CoA bisubstrate inhibitor
Components
  • Histone H4
  • Histone acetyltransferase ESA1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / acetyltransferase / autoacetylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / HATs acetylate histones / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / RNA polymerase I upstream activating factor complex / positive regulation of triglyceride biosynthetic process / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / HATs acetylate histones / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / RNA polymerase I upstream activating factor complex / positive regulation of triglyceride biosynthetic process / 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 / HDACs deacetylate histones / DNA-templated transcription elongation / histone H4 acetyltransferase activity / rDNA heterochromatin formation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / protein-lysine-acetyltransferase activity / RNA Polymerase I Promoter Escape / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / regulation of cell cycle / protein heterodimerization activity / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / DNA binding / identical protein binding / 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 ...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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / 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
CARBOXYMETHYL COENZYME *A / Histone H4 / Histone acetyltransferase ESA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase ESA1
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3053
Polymers34,4802
Non-polymers8261
Water4,252236
1
A: Histone acetyltransferase ESA1
B: Histone H4
hetero molecules

A: Histone acetyltransferase ESA1
B: Histone H4
hetero molecules

A: Histone acetyltransferase ESA1
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9169
Polymers103,4396
Non-polymers2,4773
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10070 Å2
ΔGint-18 kcal/mol
Surface area41110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.282, 183.282, 183.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#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
#2: Protein/peptide Histone H4 / K16CoA bisubstrate inhibitor


Mass: 1326.638 Da / Num. of mol.: 1 / Fragment: UNP residues 12-23 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02309
#3: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.64 Å3/Da / Density % sol: 66.16 %
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: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2011
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 30856 / Num. obs: 30856 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 42.1 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 42.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 40.4 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 12.1 / Num. unique all: 1511 / % 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: 2.1→33.463 Å / SU ML: 0.26 / σ(F): 0.19 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1547 5.03 %RANDOM
Rwork0.1886 ---
obs0.1908 30737 99.69 %-
all-30737 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.654 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 51 236 2633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082480
X-RAY DIFFRACTIONf_angle_d1.1673358
X-RAY DIFFRACTIONf_dihedral_angle_d16.059980
X-RAY DIFFRACTIONf_chiral_restr0.08351
X-RAY DIFFRACTIONf_plane_restr0.018418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16740.27481150.19412622X-RAY DIFFRACTION100
2.1674-2.24480.25931410.17742596X-RAY DIFFRACTION100
2.2448-2.33470.22771380.18652632X-RAY DIFFRACTION100
2.3347-2.44090.20171330.1892614X-RAY DIFFRACTION100
2.4409-2.56960.23971400.18492632X-RAY DIFFRACTION100
2.5696-2.73050.23511330.1952631X-RAY DIFFRACTION100
2.7305-2.94120.24841400.20182638X-RAY DIFFRACTION100
2.9412-3.2370.25241540.19422627X-RAY DIFFRACTION100
3.237-3.70480.2261570.18112667X-RAY DIFFRACTION100
3.7048-4.66570.18221530.1572692X-RAY DIFFRACTION100
4.6657-33.46680.27231430.22262839X-RAY DIFFRACTION99

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