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- PDB-2eko: Solution structure of RUH-073, a Pseudo Chromo Domain from Human cDNA -

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Entry
Database: PDB / ID: 2eko
TitleSolution structure of RUH-073, a Pseudo Chromo Domain from Human cDNA
ComponentsHistone acetyltransferase HTATIP
KeywordsTRANSFERASE / Chromo domain / Histone tail / Chromatin organization modifier / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


histone H2AK5 acetyltransferase activity / peptide crotonyltransferase activity / histone H2A acetyltransferase activity / positive regulation of mitotic sister chromatid segregation / positive regulation of protein acetylation / piccolo histone acetyltransferase complex / Sensing of DNA Double Strand Breaks / MSL complex / peptide butyryltransferase activity / histone H4K16 acetyltransferase activity ...histone H2AK5 acetyltransferase activity / peptide crotonyltransferase activity / histone H2A acetyltransferase activity / positive regulation of mitotic sister chromatid segregation / positive regulation of protein acetylation / piccolo histone acetyltransferase complex / Sensing of DNA Double Strand Breaks / MSL complex / peptide butyryltransferase activity / histone H4K16 acetyltransferase activity / lipid droplet disassembly / sperm DNA condensation / peptide 2-hydroxyisobutyryltransferase activity / positive regulation of attachment of mitotic spindle microtubules to kinetochore / peptidyl-lysine acetylation / positive regulation of triglyceride biosynthetic process / Swr1 complex / histone H4 acetyltransferase activity / regulation of double-strand break repair / Impaired BRCA2 binding to PALB2 / positive regulation of circadian rhythm / positive regulation of regulatory T cell differentiation / positive regulation of innate immune response / positive regulation of aggrephagy / Cardiogenesis / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / neural tube development / DNA repair-dependent chromatin remodeling / regulation of hematopoietic stem cell differentiation / Resolution of D-loop Structures through Holliday Junction Intermediates / negative regulation of interleukin-2 production / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / HDR through Single Strand Annealing (SSA) / peptide-lysine-N-acetyltransferase activity / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / NuA4 histone acetyltransferase complex / mitotic spindle pole / establishment of mitotic spindle orientation / Presynaptic phase of homologous DNA pairing and strand exchange / acetyltransferase activity / positive regulation of double-strand break repair via homologous recombination / spermatid development / positive regulation of myoblast differentiation / negative regulation of double-strand break repair via homologous recombination / cellular response to glucose starvation / positive regulation of autophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / cellular response to estradiol stimulus / nucleotide-excision repair / cellular response to glucose stimulus / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / DNA Damage/Telomere Stress Induced Senescence / kinetochore / cellular senescence / nucleosome / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / HATs acetylate histones / Processing of DNA double-strand break ends / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / transcription coactivator activity / regulation of cell cycle / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
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 / SH3 type barrels. - #140 / 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 / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / SH3 type barrels. / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone acetyltransferase KAT5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRuhul Momen, A.Z.M. / Hirota, H. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RUH-073, a Pseudo Chromo Domain from Human cDNA
Authors: Ruhul Momen, A.Z.M. / Hirota, H. / Hayashi, F. / Yokoyama, S.
History
DepositionMar 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase HTATIP


Theoretical massNumber of molelcules
Total (without water)9,9151
Polymers9,9151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone acetyltransferase HTATIP / 60 kDa Tat interactive protein / Tip60 / HIV-1 Tat interactive protein / cPLA(2)-interacting protein


Mass: 9915.141 Da / Num. of mol.: 1
Fragment: Histone tail binding domain, Pseudo Chromo Domain, UNP residues 5-78
Mutation: K55R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P050905-08 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92993, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.19mM Domain U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.04Johnson, B.A.data analysis
KUJIRA0.955Kobayashi, N.data analysis
CYANA1.07Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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