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Basic information

Entry
Database: PDB / ID: 1zs5
TitleStructure-based evaluation of selective and non-selective small molecules that block HIV-1 TAT and PCAF association
ComponentsHistone acetyltransferase PCAF
KeywordsTRANSFERASE / BROMODOMAIN / HISTONE-ACETYLTRANSFERASE / NMR-STRUCTURE CHEMICAL LIGAND
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / peptidyl-lysine acetylation ...regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / YAP1- and WWTR1 (TAZ)-stimulated gene expression / actomyosin / positive regulation of fatty acid biosynthetic process / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / ATAC complex / I band / cellular response to parathyroid hormone stimulus / Regulation of FOXO transcriptional activity by acetylation / limb development / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / A band / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / histone acetyltransferase binding / protein acetylation / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / histone acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / positive regulation of glycolytic process / transcription initiation-coupled chromatin remodeling / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / memory / kinetochore / Pre-NOTCH Transcription and Translation / histone deacetylase binding / positive regulation of neuron projection development / cellular response to insulin stimulus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / vasodilation / rhythmic process / heart development / HATs acetylate histones / 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 DNA-templated transcription / regulation of transcription by RNA polymerase II / 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
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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(3E)-4-(1-METHYL-1H-INDOL-3-YL)BUT-3-EN-2-ONE / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsZeng, L. / Godbole, S. / Muller, M. / Yan, S. / Sanchez, R. / Zhou, M.
CitationJournal: TO BE PUBLISHED
Title: Structure-based evaluation of selective nad non-selective small molecules that block hiv-1 tat and pcaf association
Authors: Zeng, L. / Godbole, S. / Muller, M. / Yan, S. / Sanchez, R. / Zhou, M.
History
DepositionMay 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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 PCAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2512
Polymers14,0521
Non-polymers1991
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Histone acetyltransferase PCAF / 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
#2: Chemical ChemComp-MIB / (3E)-4-(1-METHYL-1H-INDOL-3-YL)BUT-3-EN-2-ONE


Mass: 199.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2113D 13C-separated NOESY
1213D 15N-separated NOESY
2313D 13C SEPERATED FILTERED NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM sample in 100mM phosphate buffer containing 5mM perdeuterated DTT, 10% D2O10% D2O
20.5mM sample in 100mM phosphate buffer containing 5mM perdeuterated DTT, 100% D2O100% D2O
Sample conditionspH: 6.5 / Temperature: 303 K

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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 DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
ARIA2M. NILGES & S. O'DONOGHUErefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 1

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