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- PDB-1f68: NMR SOLUTION STRUCTURE OF THE BROMODOMAIN FROM HUMAN GCN5 -

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Basic information

Entry
Database: PDB / ID: 1f68
TitleNMR SOLUTION STRUCTURE OF THE BROMODOMAIN FROM HUMAN GCN5
ComponentsHISTONE ACETYLTRANSFERASE
KeywordsTRANSFERASE / LEFT-HANDED FOUR-HELIX BUNDLE
Function / homology
Function and homology information


histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / positive regulation of cell projection organization / : / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / positive regulation of cardiac muscle cell differentiation ...histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / positive regulation of cell projection organization / : / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / positive regulation of cardiac muscle cell differentiation / regulation of stem cell population maintenance / regulation of bone development / regulation of regulatory T cell differentiation / negative regulation of centriole replication / transcription factor TFTC complex / telencephalon development / histone H3 acetyltransferase activity / internal peptidyl-lysine acetylation / histone H3K18 acetyltransferase activity / ATAC complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Cardiogenesis / SAGA complex / RUNX3 regulates NOTCH signaling / limb development / NOTCH4 Intracellular Domain Regulates Transcription / regulation of T cell activation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of tubulin deacetylation / peptide-lysine-N-acetyltransferase activity / midbrain development / intracellular distribution of mitochondria / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / Formation of paraxial mesoderm / regulation of RNA splicing / RNA Polymerase I Transcription Initiation / regulation of embryonic development / histone acetyltransferase complex / negative regulation of gluconeogenesis / long-term memory / regulation of DNA repair / somitogenesis / histone acetyltransferase activity / positive regulation of gluconeogenesis / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to nutrient levels / cellular response to nerve growth factor stimulus / neural tube closure / gluconeogenesis / positive regulation of cytokine production / regulation of synaptic plasticity / multicellular organism growth / regulation of protein stability / B-WICH complex positively regulates rRNA expression / response to organic cyclic compound / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to tumor necrosis factor / heart development / HATs acetylate histones / fibroblast proliferation / protein phosphatase binding / DNA-binding transcription factor binding / in utero embryonic development / transcription coactivator activity / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Torsion angle dynamics (DYANA) for generation of initial structures; Structure-mediated assignment of ambiguous experimental restraints (SANE); Iteration between DYANA, SANE; Simulated Annealing, Energy Minimization in AMBER using full restraint set.
AuthorsWright, P.E. / Hudson, B.P. / Dyson, H.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain.
Authors: Hudson, B.P. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionJun 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4May 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


Theoretical massNumber of molelcules
Total (without water)12,2571
Polymers12,2571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 185NO DISTANCE OR ANGLE VIOLATIONS GREATER THAN 0.15 A OR 5 DEGREES
RepresentativeModel #21closest to the average

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Components

#1: Protein HISTONE ACETYLTRANSFERASE / / GCN5


Mass: 12257.139 Da / Num. of mol.: 1 / Fragment: BROMODOMAIN / Mutation: P730G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / References: UniProt: Q92830, histone acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
3233D 13C-separated NOESY
3334D 13C/15N-separated NOESY
141HNHA
151HNHB
363HACAHB COSY
NMR detailsText: Backbone assignments from HNCACB & CBCA(CO)NH (sample 2); Sidechain assignments from C(CO)NH-TOCSY & H(CCO)NH-TOCSY (sample 2); Stereospecific assignments from 13C-{13CO} & 13C-{15N} spin-echo ...Text: Backbone assignments from HNCACB & CBCA(CO)NH (sample 2); Sidechain assignments from C(CO)NH-TOCSY & H(CCO)NH-TOCSY (sample 2); Stereospecific assignments from 13C-{13CO} & 13C-{15N} spin-echo difference CT-HSQC (sample 3); Aromatic assignments from (HB)CB(CGCD)HD, (HB)CB(CGCDCE)HE, & (HC)C(C)CH-TOCSY (sample 3)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM Bromodomain, U-15N; 20mM sodium phosphate buffer; 50mM NaCl; 10mM DTT-d1095% H2O/5% D2O
20.4mM Bromodomain, U-15N,13C; 20mM sodium phosphate buffer; 50mM NaCl; 10mM DTT-d1095% H2O/5% D2O
30.4mM Bromodomain, U-15N,13C; 20mM sodium phosphate buffer; 50mM NaCl; 10mM DTT-d10100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl 6.0 ambient 293 K
250mM NaCl 6.0 ambient 293 K
350mM NaCl 6.0 ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502
Bruker AMXBrukerAMX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Instrumentscollection
NMRPipe1.7Delaglioprocessing
NMRView3Bruce A. Johnsondata analysis
DYANA1.5Guntertrefinement
SANE1Dugganrefinement
Amber6Kollmanstructure solution
RefinementMethod: Torsion angle dynamics (DYANA) for generation of initial structures; Structure-mediated assignment of ambiguous experimental restraints (SANE); Iteration between DYANA, SANE; Simulated ...Method: Torsion angle dynamics (DYANA) for generation of initial structures; Structure-mediated assignment of ambiguous experimental restraints (SANE); Iteration between DYANA, SANE; Simulated Annealing, Energy Minimization in AMBER using full restraint set.
Software ordinal: 1
Details: Structures are based upon 2232 NOE-derived distance restraints (365 long-range, 379 medium-range, 403 sequential, 1085 intraresidue, and 426 ambiguous), 155 torsion angle restraints, and 47 ...Details: Structures are based upon 2232 NOE-derived distance restraints (365 long-range, 379 medium-range, 403 sequential, 1085 intraresidue, and 426 ambiguous), 155 torsion angle restraints, and 47 stereospecific assignments.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: NO DISTANCE OR ANGLE VIOLATIONS GREATER THAN 0.15 A OR 5 DEGREES
Conformers calculated total number: 185 / Conformers submitted total number: 30

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