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- PDB-1n72: Structure and Ligand of a Histone Acetyltransferase Bromodomain -

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Basic information

Entry
Database: PDB / ID: 1n72
TitleStructure and Ligand of a Histone Acetyltransferase Bromodomain
ComponentsHISTONE ACETYLTRANSFERASE
KeywordsTRANSFERASE / Histone acetyltransferase bromodomain / 4-helical bundle
Function / homology
Function and homology information


negative regulation of rRNA processing / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / A band / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / YAP1- and WWTR1 (TAZ)-stimulated gene expression ...negative regulation of rRNA processing / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / A band / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / YAP1- and WWTR1 (TAZ)-stimulated gene expression / positive regulation of fatty acid biosynthetic process / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / actomyosin / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / ATAC complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / I band / limb development / NOTCH4 Intracellular Domain Regulates Transcription / SAGA complex / NOTCH3 Intracellular Domain Regulates Transcription / cellular response to parathyroid hormone stimulus / protein-lysine-acetyltransferase activity / negative regulation of ferroptosis / protein acetylation / histone H3K9 acetyltransferase activity / histone acetyltransferase binding / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / Formation of paraxial mesoderm / acetyltransferase activity / regulation of RNA splicing / histone acetyltransferase activity / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of embryonic development / regulation of DNA repair / histone acetyltransferase / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / positive regulation of glycolytic process / gluconeogenesis / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / enzyme activator activity / NOTCH1 Intracellular Domain Regulates Transcription / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Metalloprotease DUBs / positive regulation of neuron projection development / B-WICH complex positively regulates rRNA expression / kinetochore / Pre-NOTCH Transcription and Translation / histone deacetylase binding / memory / cellular response to insulin stimulus / mitotic spindle / vasodilation / rhythmic process / HATs acetylate histones / heart development / cellular response to oxidative stress / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / negative regulation of cell population proliferation / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A ...PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics matrix relaxation torsion angle dynamics
AuthorsDhalluin, C. / Carlson, J.E. / Zeng, L. / He, C. / Aggarwal, A.K. / Zhou, M.-M.
CitationJournal: Nature / Year: 1999
Title: Structure and Ligand of a Histone Acetyltransferase Bromodomain
Authors: Dhalluin, C. / Carlson, J.E. / Zeng, L. / He, C. / Aggarwal, A.K. / Zhou, M.-M.
History
DepositionNov 12, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionDec 11, 2002ID: 1B91
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The authors believe PRO is at both positions 804 and 805 in the wild protein sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)14,0521
Polymers14,0521
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)1 / 200
RepresentativeModel #1

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Components

#1: Protein HISTONE ACETYLTRANSFERASE / P300/CBP-associated factor / P/CAF / Histone acetylase PCAF


Mass: 14052.226 Da / Num. of mol.: 1 / Fragment: Bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCAF / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92831, histone acetyltransferase

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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
131HNHA

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Sample preparation

DetailsContents: 1mM Bromodomain, 100mM Sodium phosphate, 5mM DTT-d10, 0.5mM EDTA, pH 6.5
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglioprocessing
X-PLORBrungerstructure solution
XwinNMRcollection
ARIArefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics matrix relaxation torsion angle dynamics
Software ordinal: 1
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 1

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