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- PDB-2rnx: The Structural Basis for Site-Specific Lysine-Acetylated Histone ... -

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Basic information

Entry
Database: PDB / ID: 2rnx
TitleThe Structural Basis for Site-Specific Lysine-Acetylated Histone Recognition by the Bromodomains of the HUman Transcriptional Co-Activators PCAF and CBP
Components
  • Histone H3
  • Histone acetyltransferase PCAF
KeywordsTRANSFERASE/NUCLEAR PROTEIN / Bromodomain / Histone / Acetyltransferase / Acyltransferase / Cell cycle / Host-virus interaction / Nucleus / Polymorphism / Transcription / Transcription regulation / Acetylation / Chromosomal protein / DNA damage / DNA repair / DNA-binding / Methylation / Nucleosome core / Phosphoprotein / TRANSFERASE-NUCLEAR PROTEIN COMPLEX
Function / homology
Function and homology information


peptidyl-lysine acetylation / regulation of protein ADP-ribosylation / negative regulation of rRNA processing / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex ...peptidyl-lysine acetylation / regulation of protein ADP-ribosylation / negative regulation of rRNA processing / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / negative regulation of centriole replication / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / YAP1- and WWTR1 (TAZ)-stimulated gene expression / actomyosin / internal peptidyl-lysine acetylation / positive regulation of fatty acid biosynthetic process / histone H3 acetyltransferase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / ATAC complex / Oxidative Stress Induced Senescence / replication fork protection complex / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / limb development / A band / I band / NOTCH4 Intracellular Domain Regulates Transcription / SAGA complex / NOTCH3 Intracellular Domain Regulates Transcription / cellular response to parathyroid hormone stimulus / protein-lysine-acetyltransferase activity / protein acetylation / histone acetyltransferase binding / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / Formation of paraxial mesoderm / histone acetyltransferase activity / acetyltransferase activity / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / regulation of RNA splicing / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / Estrogen-dependent gene expression / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of embryonic development / intracellular copper ion homeostasis / regulation of DNA repair / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / CENP-A containing nucleosome / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / aerobic respiration / positive regulation of glycolytic process / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of neuron projection development / B-WICH complex positively regulates rRNA expression / kinetochore / Pre-NOTCH Transcription and Translation / memory / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to insulin stimulus / mitotic spindle / structural constituent of chromatin / vasodilation / rhythmic process / nucleosome
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Bromodomain, conserved site / Bromodomain signature. / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H3 / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsZeng, L. / Zhang, Q. / Gerona-Navarro, G. / Zhou, M.M.
CitationJournal: Structure / Year: 2008
Title: Structural Basis of Site-Specific Histone Recognition by the Bromodomains of Human Coactivators PCAF and CBP/p300
Authors: Zeng, L. / Zhang, Q. / Gerona-Navarro, G. / Moshkina, N. / Zhou, M.M.
History
DepositionFeb 3, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 6, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 13, 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 PCAF
B: Histone H3


Theoretical massNumber of molelcules
Total (without water)15,5592
Polymers15,5592
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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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: UNP residues 719-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q92831, histone acetyltransferase
#2: Protein/peptide Histone H3


Mass: 1506.771 Da / Num. of mol.: 1 / Fragment: UNP residues 32-43
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P61830
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] potassium phosphate, 100% D2O
Solvent system: 100% D2O
SampleConc.: 0.5 mM / Component: potassium phosphate / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA2.1Linge, O' Donoghue and Nilgesdata analysis
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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