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- PDB-2rnz: Solution structure of the presumed chromodomain of the yeast hist... -

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Basic information

Entry
Database: PDB / ID: 2rnz
TitleSolution structure of the presumed chromodomain of the yeast histone acetyltransferase, Esa1
ComponentsHistone acetyltransferase ESA1
KeywordsTRANSFERASE / Esa1 / HAT / chromodomain / tudor domain / RNA binding / Activator / Chromatin regulator / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / positive regulation of triglyceride biosynthetic process / 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 ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / positive regulation of triglyceride biosynthetic process / 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 / protein-lysine-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 / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / nucleosome / regulation of cell cycle / DNA repair / DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
: / 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 / Chromo/chromo shadow domain / Chromatin organization modifier domain ...: / 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 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone acetyltransferase ESA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsShimojo, H. / Sano, N. / Moriwaki, Y. / Okuda, M. / Horikoshi, M. / Nishimura, Y.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain
Authors: Shimojo, H. / Sano, N. / Moriwaki, Y. / Okuda, M. / Horikoshi, M. / Nishimura, Y.
History
DepositionMar 1, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase ESA1


Theoretical massNumber of molelcules
Total (without water)11,0721
Polymers11,0721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone acetyltransferase ESA1


Mass: 11071.521 Da / Num. of mol.: 1 / Fragment: Residues 17-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08649, histone acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1722D 1H-13C HSQC
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1mM CHROMODOMAIN [U-99% 13C; U-99% 15N], 200mM potassium phosphate, 5mM D-DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.1mM CHROMODOMAIN [U-99% 13C; U-99% 15N], 200mM potassium phosphate, 5mM D-DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMpotassium phosphate[U-99% 13C; U-99% 15N]1
0.1 mMpotassium phosphate[U-99% 13C; U-99% 15N]2
Sample conditionspH: 6.8 / Pressure: AMBIENT / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.refinement
OliviaYokochi, M., Sekiguchi, S. and Inagaki, F.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 600 / Conformers submitted total number: 20

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